In a statement, Mr Salmond denied the claims and said he has been prevented from properly challenging them by Scottish Government procedure.
Mr Salmond said: “For many months now, and on the advice of Senior Counsel, I have attempted to persuade the Permanent Secretary to the Scottish Government that she is behaving unlawfully in the application of a complaints procedure, introduced by her more than three years after I left office.
Permanent Secretary at the Scottish Government Leslie Evans has since issued a full statement in response.
“Last November, I agreed with the First Minister that, in light of wider concerns about harassment in Westminster and the Scottish Parliament, an internal review would be carried out into the Scottish Government’s procedures for handling complaints in the workplace. As part of that review, a new procedure on handling harassment complaints involving current or former ministers was introduced.
“Following the conclusion of an internal investigation I can confirm that the Scottish Government received two complaints in January in relation to Alex Salmond. Mr Salmond was notified of the complaints in March and the details of the procedure under which the complaints would be addressed.
“I informed Mr Salmond and the people involved on Wednesday, August 22 of my conclusions and that I was considering the public interest in making the fact of the complaints and investigation publically known.
“Mr Salmond was subsequently given notice that I intended to make a statement referring to the fact of the complaints.
“Following legal proceedings instigated by Mr Salmond yesterday that statement was delayed. However, given that Mr Salmond subsequently dropped those proceedings I am now able to confirm the fact of the complaints.
“I note that the former First Minister has indicated his intention to challenge the actions taken by the Scottish Government. His statement contains significant inaccuracies which will be addressed in those court proceedings. The Scottish Government will defend its position vigorously.
“You will appreciate that for legal reasons the Scottish Government is limited in what can be said.
“The First Minister has had no role in this process. I advised her of the conclusions of my investigation on Wednesday and she is of course aware that I am making this statement today.
“As the head of the Civil Service in Scotland, I have been consistently clear that there is no place for harassment of any kind in the workplace.
“In line with work already underway in the organisation to tackle inappropriate behaviour, I will consider carefully any issues about culture and working practices highlighted by these complaints.”