It's been a bruising year for the Hunter auto-electrician who was surprised, then delighted, when Kevin Rudd handed him the prestigious portfolio in late 2007.

But the bouquet turned out to be a prickly pear. Fitzgibbon's frustration with his department boiled into the open this week after the failure of army chiefs to fix a pay scandal which resulted in the salaries of SAS soldiers being docked.

He'd ordered the brass to sort it out last October. They hadn't, leaving Fitzgibbon exposed to Opposition censure. It was one of many such rows, as diverse as the timetable for this year's critically important defence white paper to the embedding of journalists with Australian troops in Afghanistan, which the military only now has reluctantly agreed to test.

Another tussle occurred over Defence's unwillingness to provide Fitzgibbon's office with the raw responses journalists had given to a survey the department was quietly carrying out on its media policy (the Defence media unit has a notoriously obstructive reputation).

Last September there was the Afghanistan "dog pen" incident, where he defended Australian troops over claims they had held Taliban prisoners in former dog pens, upsetting Muslims. It took days for the critical fact to emerge that the pens had never been used to hold dogs - it was just troop slang for makeshift enclosures.

The minister and his office have come to see themselves as some version of a David versus Goliath contest, battling Defence's ingrained habit of self-serving obfuscation. Other tensions have arisen on policy. One insider reports a dispute between minister and military over how strictly to apply Labor's election pledge to pull all Australian troops out of Iraq. The source claims Rudd got involved to resolve the issue, a claim Fitzgibbon's office flatly denies.

"I think if you did a survey of defence ministers both in Australia and around the globe, you would get a high percentage who from time to time have been concerned that the military has attempted to bypass the minister. Thankfully, that has not been my experience," Fitzgibbon insists.

Yet Rudd is acquiring, like John Howard before him, a reputation for going over his minister and dealing directly with the defence chief, Air Chief Marshal Angus Houston.

Insiders say the cumulative effect is Fitzgibbon's distrust of Houston, underscoring the irony of Houston, now in his second term as the Chief of the Defence Force, having been a long-time hero in Labor circles because of his willingness to come out and speak the truth during the infamous children overboard incident. (This related to false claims by the then defence minister Peter Reith during the 2001 election that refugees had thrown their children overboard.)

In an exclusive interview this week, Fitzgibbon couldn't contain his frustration with departmental minions. "Have I seen incompetence? Absolutely yes," he told the Herald. " Have I seen attempts to nuance information to cover for mistakes? Yes. Have I seen nuanced information in an attempt to produce outcomes that are more favourable to those who are responsible for the issue? Yes. I am sure they would be the answers from anyone who has ever served in the defence portfolio."

Such statements put his defence advisers in a difficult position. Convention dictates that the military and public servants cannot buy into public rows with the minister. In an unusual interview yesterday, Houston, widely respected for his intellect and operational nous, responded carefully: "All I will say is we do our best to provide the minister with the best and highest quality information that we can; we try and be as timely and as accurate as we can.

"Ministers often demand information in a very short timeframe. We try to satisfy their demands ? but if you have to do it quickly you don't always have the checks and balances. I would never cover anything up from the minister, ever."

Fitzgibbon's sense of mounting helplessness is not assisted by what many defence policy veterans see as the relative weakness of Nick Warner, the civilian head of the Defence Department. Warner was a skilled diplomat but is seen as a lightweight in defence policy, lacking the experience to act as an effective counterbalance to the military hierarchy.

"Nick was made secretary because Howard liked him," asserts one source with close knowledge of both men. "Joel does not need a secretary dominated by the CDF [Houston]; he needs a secretary who is independent of the CDF but collaborative."

Defence is unique among government departments because it functions as a diarchy - it has two leaders. The secretary heads the civil arm and the CDF runs the military. These two are meant to be equal. But in recent years the pendulum has tipped towards the military, now seen to be calling nearly all the shots on major defence policy, including some highly questionable hardware decisions.

"Houston is very much the senior partner," a ministerial adviser maintains. Houston denies this. "This is tired out-of-date commentary," he told the Herald. "We are a fully integrated organisation; Nick Warner and myself work side-by-side. I think we complement each other very well, we talk about everything. This notion of the military getting influence over the civilians ? it used to be very tribal; it's not tribal any more."

Allan Behm, a former senior defence official, argues the department has lost civilian policy expertise in areas such as strategic planning and force structure analysis. "The cult of the generalist does not serve public administration," says Behm. "You do need civilian policy specialists who can put the heavy rollers over the big equipment bids from the services."

Says Mike Scrafton, who served alongside Behm: " There is not the depth of understanding of strategic, tactical and operational issues on the civilian side any more."

And the former Labor defence minister Kim Beazley agrees: "The downgrade of the policy-making capacity of civilians in Defence is crippling."

Such a deficiency would pose a huge risk at a time when the Government is poised to decide on billions of dollars worth of new war-fighting capacity. Looming projects include the air force's Joint Strike Fighter ($16 billion), new submarines ($25 billion) and a fourth air warfare destroyer ($2 billion).

Fitzgibbon has been stung by perceptions he is not up to the job. There is grumbling in the bowels of Defence about having to deal with another rookie minister with inexperienced staff.

Brendan Nelson, the last of Howard's defence ministers, unintentionally came to Fitzgibbon's aid this week by publicising his own woes with Defence, claiming the military was troubled by civilian orders.

But Beazley, considered by many the most successful defence minister in the past 20 years, challenges that view. "Defence is not ungovernable," Beazley insists. "They are very responsive to someone who knows what they are doing." Perhaps predictably, he is critical of Howard's ministers who he claims "expected the department to be working for them politically, not for the country".

Some former officials believe there are cultural stumbling blocks to smoother relations between ministers and Defence. Behm recalls running a seminar for a group of senior military officers a decade ago, asking them to debate who they worked for. He got at least three different answers. "We called the first group the Cavaliers [because] they were absolutely sure that they worked for the Queen or the Governor-General," he says. "Then there were the Roundheads who thought they worked for the government of the day. Some in that group thought they worked for CDF, but since CDF thought he worked for the minister we counted them as Roundheads ? The third group we called the Maoists because they thought they worked for the people. We had a furious argument about who was the decision-maker and ultimately I had to get someone like the Vice-Chief to come in and convince them all that they worked for the minister."

When politics comes into the mix, uniformed personnel find themselves in deep conflict. Fitzgibbon's embarrassment this week was compounded by a leaked email from a sergeant-major telling SAS troops they would be disciplined if they spoke out about their docked pay.

The warning spoke of troops' obligations under the "chain of command" - the holy of holies in military organisation, it refers to taking orders from and reporting to an immediate superior in a chain that goes all the way to the top.

It's vital for safe and smooth operations during warfare. But, as Behm points out, it can be tempting for the army to invoke it as a convenient screen. "The pay of soldiers is not a chain of command issue, it's a public administration issue," he says.

Fitzgibbon is not alone in finding the relationship with his department challenging. The Herald recently spoke to more than a dozen former ministers, chiefs, secretaries and advisers about why this was so.

Hugh White, a former deputy secretary and adviser to Beazley, says it is easy for newcomers to underestimate the complexity of Defence. "It's the biggest and most complicated organisation in Australia in terms of the range of things it does, the difficulty of what it does. So right from the get-go, Defence has a different relationship with its minister than occurs with other portfolios."

Others feel a contributing factor has been a rise in the power and public profile of the CDF at the expense of the department's civilian head. This began under Howard, who came to office with a pre-existing fascination with defence that intensified when Timor erupted. Howard formed a close bond with the charismatic army general Peter Cosgrove, whom he later made defence chief.

The then PM relished cabinet get-togethers with service chiefs. Says a former adviser: "When things were really hot, he would meet them weekly, or more frequently. He became very knowledgeable about it, and was quite comfortable having direct discussions with the CDF and others on defence matters. He would let the defence minister know he had those meetings but he didn't feel the minister always had to be there."

Rudd seems to continue the pattern. Houston made a practice of directly calling David Epstein, Rudd's former chief of staff, whenever he was unhappy with Fitzgibbon's office, says a former insider. "I know that used to infuriate David because David's a real process guy."

Houston had also developed a habit of calling Fitzgibbon direct on his mobile phone, again bypassing normal protocol. "You would think for anything other than urgent conversations that really he ought to be dealing with his staff at least in the first instance so that there is some form of record," said the source.

Beazley says the cabinet's security committee, chaired by the Prime Minister, reaches "much deeper into the defence planning process than when I was defence minister". This was bad, he said, "because it diminishes the authority of the minister".

But problems arise, too, with weak ministerial offices. Some lay the blame at Fitzgibbon for failing to appoint to his personal staff people who possess defence backgrounds and expertise.

And those on the receiving end of urgent demands from ministers' offices say there is little comprehension of the time it takes to get thorough information from the frontline. "Nearly all the time it's the minister's office using the minister's name to ask for all sorts of crap," says a disgruntled administrator. "They ask unco-ordinated grab-bag all-encompassing questions without any regard to the workload."

Previous ministers, too, have been overly willing to embroil the military in political games. The children overboard incident strained the relationship between Defence and successive ministers for years.

The former army boss Peter Leahy says the relationship between the defence minister and the department has not broken down but is "finely balanced" and needs careful management. "That includes understanding from the minister and his staff that often information is not available in the form they require in the time they require it."

Beazley agrees: "One of the things you cannot avoid in running a military is that things will often be messy. Reporting systems will often be messy. The correct position will emerge. And from time to time, you will take political damage."

Joel Fitzgibbon felt that truth this week.