The privately-run airport insisted that the steel masts, which protrude from the tent-like structure, be scaled down for fear that planes descending in adverse weather conditions might clip them.
"It's in case there was an utter pea-souper. We took six inches off them," said a spokeswoman for the airport.
London City airport, which has 140 flights a day, mainly to Europe, is a mile-and-a-half from the Dome.
The airport objected at the planning stage to the building of the Dome because it feared that the height of the masts would present a hazard to aircraft.
The public body that owns the Dome, the New Millennium Experience Company, has been forced to take out insurance to cover the airport's costs in case it has to divert planes from the Dome's path.
The policy runs until 2001 and will be continued by the company that buys the Dome after the Millennium exhibition closes.
The Millennium Dome is not in the direct flight path of the airport, although planes sometimes fly over it if there is fog, thunderstorms or rain.
The airport has also insisted that the Dome should have red lights at the tops of the masts to alert aircraft flying in fog or in the dark.
The steel masts, which were made in Bolton and Bristol, are 300ft high. They were shipped to London in sections and welded together. Planners made the changes to the pylons' height before they went up, after the objections from the airport.
A spokesman for the New Millennium Experience Company said: "City airport took out an insurance policy and we pay them for it.
"The only thing that the airport insisted on was having the red lights on top."Reuse content