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The Australian Government believes the order might be completely impractical, given that commercial flights from Australia to the west coast of America are among the world's longest.
A spokeswoman for Qantas said: "The US Transport Security Administration are now requiring that passengers on flights to the US are not to congregate in groups in any areas of the aircraft, especially around the lavatories."
John Anderson, the Australian Transport Minister and Deputy Prime Minister, described the ban as "a little bit hard to handle".
Qantas said that passengers were already being informed of the new rules.
"Qantas pilots are making pre-flight announcements to this effect and cabin crew are monitoring passengers during the flight. We do not expect this to be a significant issue at all, and it only applies to flights to the United States," the airline said in a statement.
An anonymous Qantas official declined to say whether the airline had received the orders from the US Transport Security Administration, or from the Australian aviation authorities.
Qantas is among numerous international airlines that have increased security on flights over the last few weeks.
It said yesterday it was willing to accede to America's request to provide armed sky marshals on its flights to the US, a move that has been resisted in the UK by Balpa, the pilot's union.
The British Government has been deadlocked with the pilots since it hastily announced on December 28 that undercover marshals would be deployed on certain transatlantic flights.
The pilot's union fears that the low-velocity weapons that the marshals plan to use may not be safe to fire inside a passenger jet's pressurised cabin.
A set of rules governing their deployment is due to be published within the next few days in an effort to break the impasse.
America's demand that marshals be used comes after intelligence raised concerns that al-Qaeda has been planning another September 11-style attack over the Christmas period.
British Airways flights to New York and Washington, among other destinations, have been delayed as a result of the increased security measures brought in to counter the threat.
Britiash Airways Flight 223 to Washington was delayed for the fourth consecutive day yesterday as US authorities carried out background checks on all passengers. A BA flight to New York was also delayed for 20 hours.
Some countries have already chosen to refuse America's request. The Governments of Portugal, Denmark, Sweden and Finland have all said they would prefer to ground flights completely in the event of a terrorist threat, rather than have them take off with a marshal on board.
South Africa has also declined to use marshals, saying its present security measures are adequate.
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