The British airline pilots' union is demanding talks with ministers on plans to put undercover armed marshals on flights this week.
Undercover air marshals will be employed on some flights
News that marshals are being deployed pre-empted a US demand that foreign planes carry "a law enforcement officer" at certain times.
UK ministers say their move is a "responsible and prudent" response to the heightened terror alert in the US.
But the pilots' union says staff might refuse if guns are allowed on planes.
The undercover marshals are expected to begin work on Monday or Tuesday.
The Department for Transport would not say whether or not the move was linked to the US demand, which will apply to specific flights.
Earlier, Transport Secretary Alistair Darling stressed the best control was to prevent potential hijackers boarding planes in the first place.
But he told BBC Radio 4's Today programme: "It is someone who's there when obviously people have got on to the plane and are intent on trying to take over that plane. It is the last line of defence."
The government refused to comment on whether air marshals had already been used on British flights.
US Homeland Security Department spokesman Dennis Murphy said its
officials would notify foreign carriers "on a flight-by-flight basis" when it thought air marshals were
Jim McAuslan, general secretary of the British Airline Pilots Association (Balpa), said the union would be recommending that pilots stop flying unless certain conditions were met on the use of marshals.
"For a start we don't believe that guns and air travel mix," he said.
He said pilots would need to be informed if a marshal was going to be on board their plane.
"The commander needs to retain authority over the whole of the aircraft."
However, the government has said the marshals will be disguised as regular passengers.
But Mr Darling said the aircraft's captain would know if an air marshal was on the plane.
The marshals will be used on a small number of transatlantic flights where it was deemed right for the situation.
Transatlantic carriers Virgin Atlantic have declined to comment.
But a British Airways spokeswoman said: "We have always said we have concerns about having armed people on
She continued: "We feel it is best to have strong security on the ground and
that is where the focus of attention should be.
"We have always been of the opinion that if it is not safe to fly then we
will not fly."
Gwyneth Dunwoody, chairman of the Commons transport select committee, told BBC Radio 4's World At One the scheme had not been properly thought through.
"Security is not unfortunately someone waving a gun around in a pressurised machine, it is actually a rather more subtle and long-term investment," she said.
The announcement follows a number of security scares involving airports in recent days.
Last Wednesday and Thursday six Air France flights between Paris and Los Angeles were cancelled amid fears of a terror attack.
US intelligence had suggested al-Qaeda members posing a "credible threat" were due to board.
And hours later, the Delta Airlines terminal at New York's LaGuardia Airport was evacuated in a scare.
Mr Darling announced back in February that armed undercover police had been trained for use on UK passenger flights.
Transatlantic flights are likely to be the most affected
On Monday, Conservative shadow transport secretary Theresa May welcomed the move but suggested pilots should have been better consulted.
"Most passengers want the extra comfort of knowing that the pilots are entirely comfortable with it," she told BBC News 24.
Liberal Democrat home affairs spokesman Mark Oaten said everything had to be done to ensure passengers' safety.
"But the home secretary must make it clear if this is a reaction to new
evidence, or a delayed response to previous intelligence," he said.
Sunday's announcement follows similar moves by the Australian Government to use armed guards on many flights between Australia and Singapore.
Air marshals have been used in America since before the 11 September terror attacks on New York when there were just 33 sky marshals, flying mainly on international flights.