Former AFP graduate program member Adan McIntosh was sacked in July 2013 when he failed to front up for work during core business hours after senior managers found he worked 130 fewer hours than he was required to under his agreement in a two-year period.

Mr McIntosh argued he was bullied by senior managers who knew he couldn't start work at 9am because he had to take his son to school.

He later took the matter to the Fair Work Commission but it was thrown out earlier this year after Commissioner Barbara Deegan found the AFP had reasonable grounds to sack him.

Mr McIntosh was working in the AFP's information and communications technology unit when an internal audit of his timesheet and attendance records showed he had accrued more than 130 negative flex-time hours since he was hired in March 2011.

About 53 of those hours were still owed under the employment agreement in place at the time.

Senior managers expressed concerns over the discrepancy and asked Mr McIntosh to start working 8am to 4pm days to make up the hours.

In a string of emails with his supervisors over a series of months, Mr McIntosh argued working core hours was "a very primitive approach to a complex situation".

He said he had a flexible work arrangement that allowed him to start work between 9am and 10am and finish between 5pm and 6pm.

Records showed that despite repeated orders from his supervisors to begin work earlier in following months, Mr McIntosh continued to start at 10am or later, and often did not work for eight hours.

At one point he was ordered to work from 9am to 5pm, which AFP senior managers said took into account the morning school run, or he could face disciplinary action or have his contract terminated.

Mr McIntosh claimed the orders contained a "thinly veiled threat" and amounted to workplace bullying.

The dispute had also taken its toll on his health and his family.

He was stood down in May 2013 and sacked in July on grounds he failed to show up to work when directed and hadn't acted in good faith, even though the AFP said it made significant efforts to be flexible.

In handing down her decision in March, Ms Deegan slammed Mr McIntosh's attitude towards his employer as "incomprehensible".

"He made it clear that no set pattern of hours would suit him and that he should be permitted to work the hours that suited him and his personal circumstances, whether or not those hours suited the AFP," she said.

Mr McIntosh appealed that finding on grounds it was biased against him and unfair, and there were factual errors in the commissioner's decision.

The commission's senior deputy president, Jennifer Acton, this week found there were no such errors and it wouldn't be in the public interest for an appeal to go ahead.