The west London airport said in a statement that “out of respect” for the mourning period it will be making “appropriate alterations to our operation”.
These include flights being disrupted between 1.50pm and 3.40pm on Wednesday to “ensure silence over central London as the ceremonial procession moves from Buckingham Palace to Westminster Hall”.
British Airways has cancelled 16 short-haul flights due to the airspace restriction.
More flights are expected to be axed during the Queen’s funeral on Monday.
Heathrow said: “Passengers will be notified by their airlines directly of any changes to flights.
“We anticipate further changes to the Heathrow operation on Monday September 19, when Her Majesty’s funeral is due to take place, and will communicate those in more detail over coming days.
“We apologise for the disruption these changes cause, as we work to limit the impact on the upcoming events.”
Planes have already been banned from flying below a certain altitude over parts of London during the Queen’s coffin procession.
The Civil Aviation Authority said the ban has been enforced as part of wider security arrangements, and applies to “aircraft” including personal jets, small balloons, kites and parachutes.
This will create a “protective blanket” over the restricted areas, but will not affect commercial flights because they operate above the altitude limits, said a spokesperson for the regulator.
Aircraft are not permitted to fly below 2,500 feet above mean sea level within central London until 7am on September 19, with potential for this time limit to be extended.
This comes under the Restriction of Flying Regulations under Article 239 of the Air Navigation Order 2016.
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