South Africa's Sunday Times, which was first to report the story, said members of the team had pleaded to be rescued.
The ministry said that those in the team had been subject to "a number of evaluations that include background checks, reference checks, medical assessment as well as a psychometric evaluation by qualified professionals", which all members had cleared.
In a subsequent statement, the ministry added that it was "not uncommon" for individuals to have an initial adjustment when they arrive at extremely remote areas even if assessments showed no areas of concern.
It said when the vessel departed for Antarctica on 1 February "all was in order", and the incident was first reported to the ministry on 27 February.
The statement added the department "immediately activated the response plan in order to mediate and restore relations at the base".
"This process has been ongoing on an almost daily basis in order to ensure that those on the base know that the Department is supportive and willing to do whatever is needed to restore the interpersonal relationships, but also firm in dealing with issues of discipline," it said.
The department said allegations of sexual harassment were also being investigated, but that reports of sexual assault were incorrect.
The department added that a government minister was personally handling the incident, and the alleged perpetrator had "willingly participated in further psychological evaluation, has shown remorse and is willingly cooperative to follow any interventions that are recommended".
The alleged perpetrator has also written a formal apology to the victim, it said.
The Sanae IV research base is located more than 4,000km from mainland South Africa and harsh weather conditions mean scientists can be cut off there for much of the year.
The base typically houses staff who stay through the Antarctic winter for approximately 13 months.