National Air Traffic Services (Nats) changed flight patterns over parts of Surrey and Berkshire last year but without telling the airport.
When residents claimed the noise from aircraft had got worse, they were told no changes had been made.
The airport said it was "unacceptable" and processes were under review.
Nats carried out airspace trials last summer which lead to increased air traffic over communities to the south and south west of Heathrow. They finished on 12 November.
But on 27 June, it had also made changes to the Compton route - one of the six Heathrow departure routes - which are still operational.
The result is a greater concentration of flights over Virginia Water, Ascot, Binfield and parts of Bracknell, as planes now climb through a narrower airspace of seven miles (11km) rather than the previous 13 miles (21km).
The route is used by planes taking off in easterly winds and during busy times is used by about 16% of aircraft.
Swanwick
Nats's Swanwick centre typically handles about 5,000 flights every 24 hours
Heathrow Chief Executive John Holland-Kaye said: "Because of the assurances we received, we in turn told residents, in good faith, that no changes had occurred.
"That is unacceptable and I unequivocally apologise to local residents."
Amanda Smerczak, who lives in Ascot, has led a campaign to end the flights over her town.
"We are disappointed by this news but not surprised because the residents have felt very strongly that the flight paths are not the same as they were prior to the trials," she said.
"People's lives and livelihoods have been affected by these changes and we will continue to fight to return to the pre-trial flight plans."
Nats, which is based at Swanwick, near Fareham, Hampshire, said it had apologised to Heathrow for not highlighting the changes.
Heathrow said: "Nats have advised us that this change was made to improve the safe and efficient management of traffic departing from Heathrow and are not planning to revert back."
It has called on Nats to review the way it shares information with the airport on any changes which may have an impact for local communities.
The airspace trials were part of the government's Future Airspace Strategy (FAS).
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