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"This afternoon, the Prime Minister accepted the resignation of Boris Johnson as Foreign Secretary," May's Downing Street office said in a statement.
"His replacement will be announced shortly. The prime minister thanks Boris for his work," the statement said.
Since cabinet approval for the plan on Friday, however, he had refrained from public comment.
He was due to co-host a summit on the Western Balkans in London on Monday but did not show up.
Germany's junior foreign minister Michael Roth tweeted: "We're still waiting for our host".