FIA president Mohammed Ben Sulayem refused to divulge what he spoke about with Christian Horner but claimed the whole investigation saga is "damaging the sport".
Horner has been the centre of an investigation at Red Bull after allegations of inappropriate behaviour were made by a female employee.
The investigation was dismissed earlier this week with Horner being cleared of any wrongdoing.
But the saga took a fresh twist just 24 hours later when screenshots of messages allegedly between the female employee and Horner were leaked to journalists and F1 personnel.
Heading into qualifying on Friday, Horner visited both Ben Sulayem and Stefano Domenicali.
FIA president Mohammed Ben Sulayem spoke with Christian Horner on Friday
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Earlier in the day, the FIA president and Horner spoke in front of cameras after walking through the Red Bull garage together.
Horner, who has refused to comment on the file leak, has maintained his innocence throughout.
"I won't comment on anonymous speculation, but to reiterate, I have always denied the allegations," Horner said.
Details of Horner's conversation with Ben Sulayem haven't been made public, but the latter has spoken for the first time since his meeting.
"It’s damaging the sport," he told the Financial Times.
"This is damaging on a human level."
Ben Sulayem wants the focus around the sport to be more on the action with the season-opening race in Bahrain.
He added: “It is the beginning of the season. F1 is becoming so popular.
"We just need to enjoy the beginning of the season. Look at the competition.
“Why do we overshadow it with negativity?”
Horner's wife, Geri Halliwell, put on a united front on Saturday as she made her first public appearance since the allegations first surfaced.
The Spice Girl singer is said to have been 'extremely hurt' from the investigation into her husband.
Mohamed Ben Sulayem wants the focus to be on the sport now
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But she was pictured walking through the paddock hand-in-hand with Horner ahead of Saturday's race.
Mercedes team principal Toto Wolff felt the statement from Red Bull clearing Horner was "pretty basic".
"My personal opinion is we can't really look behind the curtain," he said.
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Christian Horner put on a united front with Geri Halliwell on Saturday
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"At the end of the day, there is a lady in an organisation that has spoken to HR and said there is an issue. It was investigated and yesterday the sport has received a message, 'it's all fine. We've looked at it.'
"And I believe that with the aspirations as a global sport, on such critical topics, it needs more transparency and I wonder what the sport's position is.
"We are competitors, we are a team and we can have our own personal opinions or not, but it's more like a general reaction or action that we as a sport need to assess what is right in that situation and what is wrong."
