As PRWeek went to press MSF is believed to be the only one of the 40 unnamed aid agencies to admit its workers were under investigation.
In a media statement, flagged up as the main item on its website, the MSF statement offers a condemnation of 'all forms of exploitation against vulnerable populations'.
The statement was compiled following a video conference last week with press teams in MSF's Paris and Amsterdam offices and its HQ in Brussels.
MSF head of communications in the UK Martin Broughton was one of a number of country PR chiefs to then be briefed on strategy.
He said: 'We discovered that we were mentioned on one of the reports so decided the best policy was to be as open as possible. It was decided that sooner or later the fact that we had been named would come out.'
It is understood that part of MSF's communications strategy is to make sure the media is aware that the allegations involve locally-based workers not those from the international community.
The MSF statement adds that it is in talks with the UN and STC and is awaiting further information about individual cases so that it can take action.
'We will be making every effort to follow up the risks identified in the report,' it adds.
The allegations, including reports of workers demanding sex in exchange for food, have been made by refugees in Sierra Leone, Guinea and Liberia.
Other allegations include UN peacekeepers making young girls pose nude for pictures in exchange for biscuits and children as young as four being sexually harrassed. The report contains allegations against 67 individuals.