The London Mayor's comments came during a Twitter exchange when he said: "The Scots are never going to vote for independence. These Games have done for Salmond. Vote Hoy."
This was a reference to gold medallist Sir Chris Hoy's previous statement, in which he said: "I'm Scottish and I'm British, you can be both."
SNP MSP Kenneth Gibson said: "This cack-handed attempt by Boris to politicise the Games is a serious error of judgement."