Merkel, who appeared to have inadvertently left her microphone on, could be heard talking as Johnson was making his opening remarks on Friday.
"Can you hear us Angela," he asked, chuckling, before telling her: "I think you need to mute."
The German chancellor was not the only one to suffer a blunder during the first Group of Seven video meeting, as French president Emmanuel Macron also turned up about 15 seconds late.
Johnson kicked off the meeting by waving at those on screen, saying it was "great to see all of you" before beginning the discussion.
Later in his remarks, he urged the G7 leaders to work together on "building back better" from the pandemic – using this to make a quip about US President Joe Biden.
He said it was a slogan Biden had used, adding: “I think he may have nicked it from us but I certainly nicked it from somewhere else - probably some UN disaster relief program.”
Biden could be seen laughing on the video call on the screen inside the Cabinet Room.
Johnson also expressed his hope of meeting the G7 leaders "face to face" for the summit in Cornwall in June.