A senior government source said the PM had told Ms Gray the decision was a matter for her, and the findings of her investigation were not discussed.
The source said it was now expected Ms Gray, who requested the meeting, would include pictures in her final report.
Labour suggested the “secret meeting” could damage confidence in the process.
Ms Gray has been looking into numerous gatherings reported to have taken place in Downing Street in 2020 and 2021, when Covid restrictions were in place.
Her full report is set to be published next week after the Metropolitan Police announced it had concluded its own investigation, which saw a total of 126 fines issued to 83 people.
Around 30 individuals, including the prime minister, have already been informed they are likely to be named by Ms Gray.
They have until Sunday evening to lodge any objections.
The BBC understands that Ms Gray requested the meeting with Mr Johnson over a month ago “to clarify her intentions” for what would happen after the completion of the police inquiry.
The senior government source said the meeting covered “practical and process issues”, including whether photos would be published.
On Friday, a Number 10 spokesperson said: “The prime minister commissioned the investigation led by Sue Gray and has been clear throughout that it should be completely independent.
“As he reiterated again today, the decision on what and when to publish rests entirely with the investigation team and he will respond in Parliament once it concludes.”
In a statement, Labour’s deputy leader Angela Rayner said: “Boris Johnson must urgently explain why he held a secret meeting with Sue Gray to discuss her report despite claiming her investigation was completely independent. Public confidence in the process is already depleted, and people deserve to know the truth.
“This is a prime minister incapable of taking responsibility for the rotten culture he has created in Downing Street or of doing the decent thing.
“The Sue Gray report must be published in full and with all accompanying evidence.”
An interim version of the report, published in January, did not name individuals but criticised “failures of leadership and judgement” and said some events should not have “been allowed to take place”.
The prime minister meanwhile faces an inquiry by the Commons’ Privileges Committee about whether he knowingly lied to Parliament when he previously told MPs that no laws had been broken in Downing Street.
Under government guidelines, ministers who knowingly mislead the House of Commons are expected to resign.