Timothy Patrick Cousins was yesterday sentenced in the ACT Supreme Court to 6½ years, with a non-parole period of four, for the $1.2 million swindle.

Chief Justice Terence Higgins ordered the convicted fraudster to serve half of the four years in full-time custody, with the remainder in weekend jail.

Cousins, a father who worked for the Catholic Education Office for three decades, used his position and expertise to steal the funds and cover his tracks.

The trusted employee worked the elaborate scam between 2004 and 2010, creating fake employees and ''rehiring'' old ones before funneling funds into his personal accounts. On occasions the senior payroll officer would disguise transactions as ''stipend'' payments - hard to trace amounts generally paid out to nuns and priests.

The swindle came to light after an anonymous letter arrived at the office's Manuka headquarters, alleging fraud on a significant scale.

Cousins pleaded guilty to 10 charges.

These ranged from theft of a chose in action, dishonestly obtaining property and unauthorised modification of data.

Now prosecutors will begin the task of recouping the money Cousins stole, after Chief Justice Higgins made a reparation order for the missing funds.

In the short-term, Cousins stands to lose at least his house. Last year the Director of Public Prosecutions froze the man's south Canberra home under criminal assets laws. Under the assets legislation, his conviction means the house will automatically be forfeited in two weeks. It is anticipated efforts will be made to seize a Thai getaway Cousins built with the proceeds of his crimes.

Prosecutor Joel Hiscox said the defendant ''worked the system to his advantage'' and was motivated by nothing but greed. But the man's barrister, James Lawton, pointed to his client's good character and urged the judge to impose a sentence combining full-time jail and periodic detention.

There was no evidence before the court to suggest Cousins, who had no relevant criminal history, battled with a gambling problem or significant levels of debt.

But the Chief Justice said it appeared the defendant operated under a ''delusion'' his crimes were victimless.

Cousins told the author of a pre-sentence report he ''wouldn't take a Cherry Ripe from Woolworths'' but had a ''Robin Hood syndrome'' when it came to his employer. ''I've gone from being a golden-haired boy to, if they couldn't trust me, who could they trust,'' he told the author.

The swindled money was reportedly spent on braces, surgery, school fees and the house and land in Thailand.

Chief Justice Higgins described Cousins' behaviour as ''a sophisticated fraud perpetrated on the Catholic Education Office and repeated, time and time again''. In sentencing, he took into account the need to send a strong message of denunciation, but reduced the sentence because of the man's guilty pleas and prior good character.

But the judge noted he was able to pull off the theft ''by reason of the position of trust that he held and of course by reason of his apparently trustworthy character and nature''.

In a statement yesterday afternoon the Catholic Education Office's deputy director, Mark Hogan, said steps had been taken to ensure similar theft could not occur again.

The court heard the office's own investigation into the fraud cost $60,000, and their former employee's conduct also cast a shadow over the organisation.

''Staff and school community members have done a great deal to put this matter behind them and to move forward in an environment characterised by ethical, honest and transparent behaviour,'' Mr Hogan said. He said the sentence had brought ''closure and relief'' to the office and the Archdiocese of Canberra and Goulburn.