The paper reports that the chef stepped back from Marylebone’s The Royal Oak in November while an external firm, HR180, investigated claims he had "harassed female staff by asking for sexual intercourse and oral sex".
Doherty was found guilty of "misconduct" and apologised to staff in a meeting last month.
It is understood he remains involved with the pub, but his role has changed from head chef to executive chef and he will not oversee the daily running of the kitchen.
Doherty said in a statement to The Sunday Times: “I would never intentionally make offensive comments to anyone I work with, female or male. I have apologised to the whole team for any offence I may have inadvertently caused. It would never by my intention.”
The chef appeared as a judge on the BBC show Britain's Best Home Cook last year, but wrote on Twitter today that he would no longer be involved in the programme.
Doherty left his executive chef role at London's Duck & Waffle restaurant in April last year, before taking on The Royal Oak as his first solo venture in June. He is also partnering with London catering company Rhubarb on its upcoming New York restaurant, set to open this year.
Urban Inns Limited, which runs The Royal Oak, told The Sunday Times: “We take allegations of misconduct in any form very seriously and we used an independent HR company to thoroughly investigate some suggestions of inappropriate communications.
“Urban Inns Limited has acted, and continues to do so, on these recommendations, following which Dan returned to work.”
Gemma Bell PR, which previously handled press for The Royal Oak, said it had terminated its contract with Urban Inns Limited after the allegations came to light on 25 January.
The PR company said in a statement: “It transpires that Urban Inns Limited kept us in the dark about these allegations, Dan’s suspension and return to work. We are obviously appalled by what we have heard both of Dan’s conduct and the way in which it has been handled.”
BigHospitality has contacted The Royal Oak for further comment.