Sergey Lavrov denied claims the Kremlin had interfered in democratic elections online and accused Mr Johnson of being a “hostage” of untrue Western “narratives”.
When the Russian foreign minister told a press conference in Moscow that Mr Johnson himself had confirmed Russia had not interfered in the UK’s election and Brexit referendum, the Foreign Secretary interrupted: “Not successfully.”
The clash came after Mr Johnson issued a warning to the Kremlin that Britain was “prepared and able” to respond in kind to cyber attacks.
Speaking after more than an hour of talks on the first visit to Russia by a British foreign secretary for five years, both men acknowledged that relations between the two countries were at their worst for many years.
The two men insisted they had established a level of personal trust, with Mr Johnson joking that he had even handed his coat with “everything in my pockets, secret or otherwise” to Mr Lavrov when he arrived at the Ministry of Foreign Affairs building.
Mr Lavrov joked back: “I can say that there was nothing in the pockets of Boris’s coat.”
Mr Johnson responded responded: “So you have searched it already?”
However, when Mr Johnson rejected Mr Lavrov’s denial that Russia had attempted to interfere in British polls, the Russian foreign minister retorted: “He is afraid if he doesn’t contradict me his reputation is going to be ruined.”
Mr Johnson said Russian attempts to interfere in Britain’s referendums and elections “whatever they might be” had not been successful, adding that if they had, “that would have been an entirely different matter”.
Mr Lavrov said the evidence produced so far of Russian attempts at interference amounted to no more than the spending of “a few kopecks” on social media adverts.
“I think you have made all this up in your Western community and unfortunately right now you are hostage to this subject, it is very difficult for you to climb down from the fence you have climbed.”
He criticised Britain for cutting off ties with the FSB security agency over the murder of Alexander Litvinenko in London, complaining that UK authorities had refused to hand over information in the case.
He said the takeover of Crimea had been approved by a referendum of its citizens unlike the break-up of the former Yugoslavia
And he said that UK Government criticism of politicians who speak to Russian media outlets like the RT TV channel did not reflect well on the UK.
“We are concerned that the cradle of democracy, the United Kingdom, sees the vilifying of people for speaking to Russian media.
“It doesn’t add to the good reputation of the Government, unfortunately.”
Earlier Mr Johnson was rebuked by his host for speaking in public about their differences.
On the eve of the talks, Mr Johnson sent a blunt message to the Kremlin to stop its use of cyberspace to disrupt Western countries.
He told reporters: “The UK is certainly prepared and able to respond, should we so desire.”
Additional reporting by the Press Association