The aviation safety regulator believes Virgin Australia is rostering pilots “closer to the limits” of anti-fatigue standards, amid fears some are working 12-hour days back-to-back but are hesitant to report feeling tired out of fear of losing shifts.

Civil Aviation Safety Authority (Casa) officials’ comments at Senate estimates on Wednesday evening followed revelations in the Guardian that pilots had repeatedly raised concerns over Virgin’s rostering system adding to fatigue levels.

As Virgin Australia and the Transport Workers’ Union (TWU) remain in a standoff over a proposal to strip pilots of six days’ annual leave during negotiations for a new enterprise agreement, email chains between pilots and management as well as pilot-only discussion groups raised frustration at what they allege was management’s failures to recognise the fatigue issue.

The correspondence seen by Guardian Australia revealed anger at outdated roster software which they claim has not been replaced despite a promise to do so by the owners of the airline, private equity firm Bain Capital. In addition, there is an alleged reliance on routinely scheduling pilots to work maximum shift lengths – 12 hours and longer in the event of delays – on back-to-back days, while allowing for just the legal minimum rest period of 12 hours.

Matthew Bouttell, the executive manager of Casa’s regulatory oversight division, responded to questions from Labor senator Tony Sheldon about the pilots’ concerns, as well as the results of a TWU survey of 180 pilots – of the roughly 1,000 who work at Virgin – which showed that 85% said the rostering system had affected how they manage their fatigue.

Bouttell and fellow Casa leaders explained that while there are strict maximum shift lengths and minimum recovery periods for smaller air operators, more mature airlines such as Virgin have bespoke fatigue risk management systems approved by Casa that could lead to slightly longer days for pilots because of other mitigating strategies.

However, Bouttell conceded Casa believed Virgin’s rostering system had been nearing approved fatigue limits.

“There’s been adjustments to their roster where they’re getting closer to the limits of that fatigue risk management system,” he said.

Bouttell also said that, in the last 28-day pilot roster period, “we understand that 45 crew removed themselves from duty due to fatigue” – a figure which represents just under 5% of pilots at the airline.

Bouttell said pilots self-reporting fatigue and refusing a shift was a “great example” of the airline’s fatigue risk management system working.

Sheldon then noted “there’s a wealth of advice to say the pilots’ capacity to make an individualistic decision is extremely limited”.

In addition to concerns that self-reporting fatigue leads to less pay if they refuse a shift, reported by Guardian Australia, Sheldon noted the potential for pilots to fear that repeatedly turning down shifts could adversely affect how their manager sees them.

Steve Campbell, the executive manager of national operations and standards at Casa, responded that “we’d be very concerned if pilots did have that sort of repercussions for walking off or reporting fatigue, that’s where we would be very concerned”.

“I’m not aware of any of that [at Virgin],” Campbell said.

Pip Spence, the chief executive of Casa, said that after “we saw the article that was in the press on Friday, we engaged closely with Virgin”.

“We’ll continue to explore to make sure that there is nothing that’s being done that shouldn’t be done.

“[But] it can’t be down to the individual. The system has to actually support safe outcomes.”

Under Virgin pilots’ current enterprise agreement, which lapses at the end of June, pilots are entitled to 12 days off every 28-day roster period, of which there are 13 periods a year. Virgin Australia is proposing that for six of the 13 roster periods, days off would be cut to 11. The TWU survey of 180 pilots found that 93% intend to vote no to the proposed deal and 88% are specifically unhappy at the planned reduction in days off.

Under the proposed deal – which has been agreed with the Australian Federation of Air Pilots, a union which represents a majority of pilots at Virgin – pilots would receive a 9.38% pay rise in the first year, and 3% rises in the second and third years, in return for the loss of the six days off.

Critics of the proposed deal, including the TWU, note that pilots accepted a 17% pay cut for the last enterprise agreement to help the airline’s pandemic recovery.

Virgin Australia was contacted for comment. Responding to questions from Guardian Australia last week, a Virgin Australia spokesperson said the airline “operates under a robust fatigue management system approved by the Civil Aviation Safety Authority” in “extensive consultation with pilots”, adding that “our pilots have the highest number of rostered days off in the industry at 156 per year”.

Spence, later in the estimates hearing, said that a review of the fatigue management system would begin within the next 12 to 18 months.