The move comes after a string of similar incidents and amid tense relations with Moscow over the conflict in Ukraine and a London inquiry into the poisoning of former Russian spy Alexander Litvinenko.
The Ministry of Defence said such incursions by Russian planes were currently running at around one a month and that the latest happened off the south coast of England.
"Russian aircraft manoeuvres yesterday are part of an increasing pattern of out of area operations by Russian aircraft," the Foreign Office said in a statement. "While the Russian planes did not enter sovereign UK airspace and were escorted by RAF Typhoons throughout the time they were in the UK area of interest, the Russian planes caused disruption to civil aviation.
"That is why we summoned the Russian Ambassador today to account for the incident."
The defence ministry said that the planes involved in the latest incident Wednesday were Tupolev Tu-95 bombers, known by their NATO classification as Russian "bears".
A spokesman for the Civil Aviation Authority, which regulates aviation, said he was "not sure where this idea has come from" that there had been disruption to civil aviation.
He suggested it may have been the two British Typhoons which caused any disruption as they may have flown through airspace near Bournemouth, southern England, where there is a small civilian airport.
"It was probably two Typhoons that were scrambled to intercept that caused some disruption," he said.
In November, four Russian navy warships were spotted sailing through the English Channel and were accompanied by a Royal Navy patrol boat.