Red Bull investigate Horner over 'inappropriate behaviour' allegations
It is understood the allegation was made by another member of staff for the British-based team, which last year carried Max Verstappen to his third consecutive world championship.
Horner, 50, who has been Red Bull team principal since 2005, strongly rejects the accusation.
"After being made aware of certain recent allegations, the company launched an independent investigation," Red Bull, the Austrian energy drinks firm which owns the F1 team, said in a statement.
"This process, which is already under way, is being carried out by an external specialist barrister.
"The company takes these matters extremely seriously and the investigation will be completed as soon as practically possible. It would not be appropriate to comment further at this time."
Horner has overseen seven drivers' world championships and six constructors' titles.
Red Bull won 21 of the 22 races staged last year, with Verstappen setting a record of 10 consecutive victories as he cruised to his third straight title.
Red Bull are due to launch their latest car on February 15 ahead of the new season, which starts in Bahrain on March 2.