Alex Rowley has been suspended by Scottish Labour pending an invesitgation into allegations about his personal conduct.
The move came after he stepped aside as interim leader of the party to allow an investigation to take place.
Mr Rowley has denied the allegations, made by a former partner to a national newspaper, that his behaviour made her life hell.
The senior political figure – a former leader of Fife Council – referred himself to the party to allow the investigation to begin.
The decision to suspend him from the party was confirmed by its business manager.
James Kelly said: “It is important that the investigation into these allegations is fair and transparent, and the matter will be thoroughly investigated using the Labour Party’s internal complaints procedure.
“However, in light of the serious nature of the allegations, Labour at Holyrood has taken the decision to remove the whip from Alex Rowley for the period of this investigation.”
Senior figures within Labour have also spoken out.
Kezia Dugdale, whose decision to stand down as leader saw Mr Rowley take over at the helm pending an election, backed the suspension move. She called the allegations “serious and deeply concerning”.
She said: “Sexual harassment and abuse is never acceptable. If the past weeks have taught us anything it is that we need to support victims of abuse and all allegations need to be taken seriously and investigated in a fair and transparent way.”
In a statement, Mr Rowley said: “I totally refute these allegations and will take all steps necessary to clear my name.
“These allegations must be properly and thoroughly investigated in line with our party’s procedures – and I will refer myself to the party so such an investigation can take place.
“While that investigation is carried out, I will step aside as deputy leader, as well as interim leader, of the Scottish Labour Party.”