Talks focused on issues being discussed at the G7 summit, but Emmanuel Macron also raised his vision for a European political community.
The two leaders met at the G7 summit in Germany but did not address the situation which has seen more than 12,000 people make the crossing so far this year.
Meanwhile, despite the Elysee Palace insisting Mr Johnson expressed interest in Mr Macron’s vision for a wider European political community incorporating non-EU states such as the UK, Downing Street stressed there was no prospect of a return to free movement across the UK’s borders.
The talks at Schloss Elmau in the Bavarian Alps focused largely on issues related to the G7 summit, No 10 said.
Asked why the boat crossings were not raised, the Prime Minister’s official spokesman said: “There are very significant issues of geopolitical concern to discuss, not least the crisis in Ukraine.
“They have talked about those issues previously and I’m sure they will again.
“But, obviously, on the eve of the G7, that’s pretty much, I’m sure, at the forefront of both of their minds.”
The Elysee said Mr Johnson showed interest in the French President’s vision for a wider European community, something that was not mentioned in No 10’s account of the meeting.
The Prime Minister’s official spokesman said: “We’re happy to discuss this with the president and EU colleagues, should they provide further details on on this.”
Mr Macron’s idea would open the door to closer ties with the EU for countries outside the bloc including Ukraine, the UK and the nations of the western Balkans, covering areas including “the movement of people”.
However, No 10 pushed back against any suggestion the UK would return to pre-Brexit free movement of people.
“As far as I’m aware of, the Prime Minister hasn’t had any formal details put to him on that.
“It would be fair to say that there’s no plans to change our position with regard to freedom of movement, control of our borders, that’s not going to change.”
Asked why the discussions were not mentioned in Downing Street’s account of the meeting, the spokesman said: “It’s not unusual that readouts can differ slightly.”
The spokesman also said he was “not aware of” any discussions at the meeting in relation to the trouble faced by Liverpool fans at the European Champions League final in Paris.
Mr Johnson’s spokesman said the meeting between the two leaders was a “cordial” one “between two people who know each other very well”.