The clash happened on an official visit to Russia designed to thaw relations which are at their lowest for years.
At a press conference, Russia’s foreign minister Sergey Lavrov denied claims that Kremlin-sponsored hackers had intervened in democratic elections and said that was confirmed by his British counterpart.
But before an audience of journalists and diplomats, Mr Johnson interrupted saying, “Not successfully – not successfully is the word.”
Mr Lavrov insisted the “Western community” had fabricated the story and Mr Johnson had become “hostage to this subject” meaning it was “very difficult for you to climb down from the fence you have climbed.”
He used the event to attack the UK for cutting ties with Russia’s security agency after the fatal poisoning of former KGB man Alexander Litvinenko in London in 2006.
And he defended Russia’s illegal seizure of Crimea from Ukraine on the grounds it was backed by a referendum.
Mr Johnson said there was “abundant evidence” of Russian interference in polls in the US, Germany, Denmark and France.
The Kremlin was accused of interfering in the Brexit vote after it emerged there were more than 400 fake Russian-linked Twitter accounts publishing posts.
Earlier, Mr Johnson warned Moscow against launching cyber attacks, telling reporters: “The UK is certainly prepared and able to respond, should we so desire.”
Mr Lavrov criticised Mr Johnson for not being more discreet, telling him: “It is no secret that right now our relations are at a low point. We would prefer to talk about our mutual concerns not before a mic, but directly.”
However, Mr Johnson also said the two countries should emulate their Second World War predecessors to cooperate on global security issues despite their differences.
Mr Johnson insisted he had not gone to Russia looking for a fight but “it’s important to deliver tough messages about the difficulties we have with Russia and not shy away from them.”
He called for efforts to “rebuild a sense of trust between the populations”.