The Russian foreign affairs department said it contacted the Swiss ambassador in Moscow to express its concerns after an F/A18 jet belonging to the Swiss airforce made a "dangerous approach" to a plane carrying a Russian parliamentary delegation to Geneva.
The department said the incident could not be explained away as being part of "standard procedures" and said Switzerland should have warned Russia of the manoeuvre.
Switzerland has admitted that one of its warplanes approached the Russian plane carrying a delegation headed by parliament speaker Sergei Naryshkin.
The incident reportedly occurred in air space above the Swiss city of Biel/Bienne in the canton of Bern.
Moscow initially complained about the incident to France, mistaking the warplane's nationality and angrily summoning the French ambassador on Monday.
In response, the French foreign ministry summoned the Russian ambassador in Paris Tuesday and "condemned the fact that our ambassador to Moscow was summoned."