A Border Force spokesman said: "We will not compromise border security but we always aim to keep disruption to a minimum by using our staff flexibly to meet demand."
Travel expert Simon Calder has told London Tonight that the queues at Heathrow have been caused by border officials being forced to carry out rigorous checks, regardless of the risk profile of the passengers that are arriving.
He said that they were effectively "working to rule" even though "they know from years of experience that actually the vast majority of passengers coming in through Terminal 5 are no threat whatsoever and they would rather be focusing on the flights they believe are of particular interest."
He added: "To be stuck in a queue for two, three, maybe four hours, as we saw some poor passengers on Friday night, is really not good enough.
"There are various solutions that could be proposed to this - including throwing more money at it or training more people - but in the short term the only thing to do is to let people through more quickly on certain flights."
Lengthy queues at Heathrow cleared overnight - but further concerns were raised today about the reputation of the airport with the Olympics on the horizon.
Keith Vaz, chairman of the Home Affairs Select Committee, told BBC Radio 4's Today programme: "There is a real problem and the problem has emerged over the last few months.
"I'm not saying we should abandon checks, but it's a choice for the Government - you either look at the way you deal with people when they arrive at Heathrow or you recruit more staff.
"This is not just about the Olympics, this is about what happens before and after, it's about Heathrow as a world-class airport and it's about our reputation, and we need to make sure we get it sorted."
A spokeswoman for BAA, which owns Heathrow, said Friday night's long queues, which saw passengers waiting for up to an hour, had cleared by midnight.
Discussing the situation today, she said:
– BAA Spokeswoman
"Everything is looking quite good in the immigration halls. Things are moving and we haven't got major queues.
"The Border Force is putting staff where they are needed at the moment."
Immigration Minister Damian Green is to be grilled by MPs about queues at Heathrow amid concern that the issue is doing "huge damage" to Britain's reputation.
Keith Vaz, chairman of the Home Affairs Select Committee, announced the move after reports of long delays at passport control on Thursday night and Friday night.
Alastair Campbell, who was caught up in the queues, tweeted: "If this is what Heathrow T5 border queue is like on an average Thursday, Olympic athletes should think about coming soon."