The mayor of London's decision to back the "Leave" campaign was a particular blow to the Prime Minister, whose friendship and rivalry with Mr Johnson stretches back to their days at Eton and Oxford.
He said at the time that he hoped for a "reasonable. civilised argument" with someone he considered a "great friend".
But in an interview with Glamour magazine, he conceded that the political division had dented that bond.
"I'm still friends with Boris, just perhaps not such good friends," he said.
He said it was "frustrating" that Mr Johnson - and another close ally, Justice Secretary Michael Gove - had chosen to campaign on the opposite side in the battle over the UK's future relations with Brussels.
"I think they have made the wrong decision, but they're politicians and they have to decide," he said.
In the interview - in the June issue of the magazine due to be published on Thursday - Mr Cameron also renewed his insistence that he would not quit as PM if the country backed Brexit and said he did not expect the debate to end if voters supported staying in.
"Europe will remain a more compelling issue than any other for some people. I'm not expecting Nigel Farage, for example, just to go and play golf," he said.
Claims Brexit would improve border controls were "a total myth", he said.
"Right now, we can check every single person, every single car coming in.
"People who want to come to work in Britain have the right to come to work. But if we think someone is a security risk, we can turn them away, and we have turned away some 6,000 people since I've been PM."
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