British Airways will move most of its flights over the next year
Cancelled flights, baggage delays and a temporary suspension in check-in have blighted the opening day of Heathrow's new £4.3bn Terminal 5.
British Airways, which has sole use of the terminal, cancelled 34 flights due to "teething problems" and was later forced to suspend passenger check-in.
Technical difficulties also meant major delays in reclaiming luggage.
BA blamed the glitches on problems with "staff familiarisation", which had a knock-on effect on bags and flights.
A BA spokeswoman said delays in getting staff screened for work and other technical difficulties had caused the airline problems.
Cancelled services in and out of the terminal included flights to Munich, Frankfurt, Paris and Brussels as well as Glasgow and Aberdeen.
"These are all domestic or short haul flights and we are working hard to get people away on alternative flights," a BA spokesman added.
One passenger in a wheelchair was stuck on a flight arriving into T5 from Glasgow for more than an hour - and then when he was transported to the terminal he realised he could not get up the kerb.
"I couldn't even get into the building without getting up a step," Matt Duffy told the BBC.
"It is totally unbelievable as far as I am concerned."
Passengers departing from and arriving at the new terminal also suffered delays retrieving their bags.
Some waited two hours for luggage from a Frankfurt flight that landed at around 0830 GMT.
And in Paris, BBC reporter Peter Grant said no bags had made it on to his morning flight from Heathrow.
Airport operator BAA, which operates the baggage distribution system at T5, said a total of three flights had left the terminal without luggage on board due to a system fault.
Danish businessman Henrik Moeller, who travelled from Hamburg and landed at T5 at 0745 GMT, said he was not reunited with his bags until 0900 GMT.
"I have read about this new bag system and how it was supposed to be so much better. It's obvious there have been teething problems."
Anja Kaut, arriving from Munich with her husband Matthew and 10-year-old daughter, Charlotte, also had to wait about an hour for their luggage.
"We were told there was a technical defect," said Mrs Kaut.
But those departing also suffered problems.
Heather Stevens's partner Neil Stonebridge was due to take off from T5 for Los Angeles at 1005 GMT. Almost three hours later the plane was still at its stand waiting for passengers' baggage to be loaded.
Heather, 36, told the BBC: "Apparently the computer software told the baggage people that the flight had taken off.
BA TERMINAL CHANGES
27 March: Domestic and most European flights move from Terminal 1 to T5
27 March: Long-haul flights from Terminal 1 move to T5
27 March: Miami service moves from Terminal 3 to T5
30 March: Algiers moves from Gatwick to T5
30 April: All Terminal 4 long-haul go to T5 (except Singapore, Bangkok and Sydney)
17 Sept: Barcelona, Madrid, Lisbon, Nice and Helsinki move from Terminal 1 to Terminal 3
Early 2009: Singapore, Bangkok and Sydney move from Terminal 4 to Terminal 3
"So everyone in the plane just watched as all their suitcases were taken back into the terminal instead of being loaded on."
One baggage worker told the BBC the situation was "mayhem" and that the technical problems had been known about for some time.
"They have been doing tests on the belt system for the last few weeks and knew it wasn't going right. The computer cannot cope with the number of bags going through."
There were also complaints from passengers about confusing road signs, problems when paying at a car park, and broken down escalator.
In a statement, BA said it had experienced "initial teething problems" first thing in the morning, which had caused delays in staff arriving at their posts.
Difficulties included car parking provision, delays in staff security screening and staff familiarisation and "some baggage performance issues", it said.
"These delays have had a knock-on effect during the day so we have taken the decision to cancel a very small number of flights. We would like to apologise to passengers for any disruption to their flights," the statement added.
Earlier the company said such problems were "not unexpected following one of the most complex and largest airport moves in history".
Aviation analyst Jamie Bowden told the BBC teething problems were to be expected on the opening of a terminal, with new airports in Japan and Hong Kong also suffering difficulties in their first days.
What was important was that BA and airport operator BAA worked together to solve the technical problems "quickly" to ensure the minimum disruption for passengers, he added.
Earlier, anti-airport expansion groups held a protest at the new terminal.
Environmental campaigners in red T-shirts staged a peaceful protest
Hundreds of protesters - wearing Stop Airport Expansion T-shirts and opposed to plans for a third runway and sixth terminal at Heathrow - carried out a peaceful protest.
Among the protesters at the airport were Hazel, 71, and Jock Cooper, 72, who have lived in Old Windsor - under the flight path - for 45 years.
"It's a stupid idea to sign an agreement in Bali saying we want to save the planet and then we read there was going to be a third runway," said Mrs Cooper.
"The area, skies and planet won't take it."
BAA says the opening of T5 will not see any more flights operating to and from Heathrow, but environmental groups say more noise, pollution and stress will result.