The British Air Transport Association has written to Theresa May with 11 airlines’ concerns over possible delays at peak travel times such as Easter.
They say there are too few border staff for full security checks.
But the Border Force said it had a “very solid plan” in place and disruption would be kept to a minimum.
It said it was recruiting extra staff to help with the holiday demand.
British Airways and Virgin Airlines are amongst those expressing their concerns over potential delays to hundreds of thousands of passengers.
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The problems with the UK Border Agency (UKBA) stem from a decision last year to relax certain extra passport checks.
This was agreed with the Home Secretary, but UKBA chiefs went further than the government had anticipated, and abandoned some checks altogether.
As a result ministers ordered full checking be restored.
The problem is that the UKBA had reduced staffing levels because the less stringent checks needed fewer officers at passport control – and so there are now staff shortages.
The airlines are warning this poses risks to their operation, and to the experience of passengers.
Heathrow Airport sources say on occasion queues have reached 3 hours in Terminal Four’s passport control for passengers arriving from non-EU countries.
What’s less clear is whether travellers can expect disruption over Easter.
More than 370,000 passengers will fly from Heathrow airport between Good Friday and Easter Monday, and 200,000 will travel through Gatwick.
Simon Buck, of the British Air Transport Association, which represents the airlines, urged Mrs May to bring in more staff to cope with the demands of making full and thorough security checks for an increased number of passengers over Easter and the Queen’s Jubilee.
He said the stringent checks would be “more time consuming” and asked for “a reassurance from the government that the UK Border Agency is being properly resourced”.
There was also concern that the impact on airport operations could lead to “congestion” in baggage halls and passengers being kept on flights.
But head of the UK Border Force, Brian Moore, denied there would be gridlock: “We plan very carefully for peaks in demand, we’ve been working closely with the airlines around this.”
He added that “getting through this safely” was a clear priority.
Meanwhile, the Home Office said it would not comment on the number of current border staff for “security reasons”.
The Immigration Service Union said about a third of the workforce had been cut over the past five or six years, and that many of the extra workers brought in by the Border Force would be staff asked to work on their rest days.
The union also said some staff would come from a contingency pool of workers who had taken redundancy or retired.
However, a Home Office spokesman denied the claim, saying extra officials who would be working over the Easter period would be “back-office” staff.
The spokesman said it had not yet implemented a contingency plan – set up to cope with the Olympics – which would involve former workers being employed on short-term contracts.
Border staff previously used “risk-based” passport checks on people coming into the country, which involved not carrying out extra checks on passengers.
After years of reducing front line staff, returning to a 100% check system will undoubtedly mean lengthy queues at UK airports over critical holiday periods such as Easter and the Diamond Jubilee”
Virgin Airlines spokesman
These include scanning the passport biometric chip and checking government warning lists.
But following criticism over the use of these “risk-based” measures, the government has now asked for all mandatory checks to be carried out – which take longer.
A spokeswoman for Virgin Airlines warned of disruption and called for the government to provide more resources: “After years of reducing front line staff, returning to a 100% check system will undoubtedly mean lengthy queues at UK airports over critical holiday periods such as Easter and the Diamond Jubilee.”
Heathrow Airport said the coming weekend would not be the busiest of the Easter getaway.
A spokesman said last weekend was busiest for departures and that Sunday 15 April will be the busiest for arrivals. He also said severe disruption was not being predicted.
John Holland-Kaye, commercial director of Heathrow owner BAA, added that immigration waiting times were currently “not a good enough welcome to the UK”, and said the Home Office was ultimately responsible for staffing levels.
Shadow immigration minister Chris Bryant said job losses at the UK Border Force were “leaving the security of the UK exposed”.
He added: “With a cut of over 5,000 staff promised by the next election, the home secretary is leaving our borders dangerously understaffed, just when the UK is expecting record numbers of arrivals for London 2012.”
But the chairman of the Home Affairs Select Committee, Keith Vaz, said there was an “opportunity” for the home secretary to solve problems, underlining that it was “absolutely essential we get this right” in time for the Olympic Games in July.
The Border Force became a separate law-enforcement body in early March, as a result of the UK Border Agency being split in two.
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