The cutbacks to the Air Security Officer program – created as a last-ditch defence against hijackers following the attacks of September 11, 2001 – will see the number of marshals on some 747 flights cut by a third.

There will also be a reduction in the rest periods officers will be allowed at the end of long-haul flights and a system of rotation that will see staff seconded to other areas of the Australian Federal Police for periods of three months.

Concerns over flight deck protection

Speaking on conditions of anonymity, several aviation industry experts told The Australian newspaper they had concerns about the ability of ASO teams to protect the flight deck – their primary mission – if their numbers were cut.

There are 130 highly-trained, armed security officers available to patrol domestic and international flights, the AFP said yesterday, with the marshals travelling incognito on certain domestic and overseas flights, their presence known only to the captain. At a minimum, they travel in teams of two, although on long-haul flights the number is often higher.

The ASO program was launched in 2001 by the Australian Protective Service, which was integrated into the AFP a year later.

In 2003, an ASO disarmed a 68-year-old homeless man brandishing a Stanley knife on board a flight from Sydney to Cairns – apparently the only occasion in Australia where a sky marshal is known to have acted on a threat.

Government has no comment on "classified" program

While the Australian and International Pilots Association promised to monitor the changes for signs they have undermined security, Flight Attendants Association International division secretary Michael Mijatov said his organisation had not been advised of the cuts.

Opposition justice spokesman Christopher Pyne attacked the cuts, although they were initiated during the time of the Howard government. "Unless they have information that the terrorist threat has diminished, it's potentially playing with people's lives to reduce ASO teams," he said.

Home Affairs Minister Bob Debus declined to comment, saying the program was classified.

It is understood the changes are consistent with the recommendations contained in a report commissioned by the AFP in June last year and conducted by a private security consultancy.

The AFP confirmed certain "tactical considerations" of the program had been changed, but would not elaborate.

A spokesman said a number of reviews had been conducted.

"Those (reviews) identified aspects of the program that could be refocused to better align it with the contemporary aviation security environment," he said. The AFP said the changes would not result in any reduction in the 130 deployable ASOs. Nor would there be any reduction in the program's budget of $135.5 million over the 2006-2010 period.

The spokesman said the presence of ASOs on flights was determined according to risk and available intelligence.

Australian and International Pilots Association general manager Peter Somerville confirmed he had been advised of the changes. "Our discussions with the AFP have given us some more confidence in those changes, but we remain, overall, cautious about what it might mean for the program and what it might mean for the pilots who are operating flights with ASOs."

Mr Somerville said the minimum rest period for Qantas pilots on Australia-Los Angeles trips was 34 hours. Industry sources said it was understood ASOs would now get about 24 hours of rest, down from 48 to 60 hours.

Mr Somerville said there could be a case for shorter rest periods if it meant keeping the officer on the same time zone, thereby reducing fatigue.

Executive director of the Australian Homeland Security Research Centre Athol Yates said he was not surprised to hear of the changes to the program, which he said was of "questionable" security value. "Hardening the cockpit doors and changing the protocols for hijacking has made it harder for terrorists to get weapons on board an aircraft and take control of it," he said.