There has been concern over women in the Northern Isles having to travel to Aberdeen for examinations.
Justice Secretary Michael Matheson announced NHS Education Scotland (NES) would receive Â£76,000.
This will be used to review training and fund up to 50 places for doctors to complete the accredited course.
Speaking in Shetland, Mr Matheson said: "It is vitally important that we do all we can to ensure that the process of gathering evidence of rape or sexual assault doesn't cause more trauma to victims.
"I am pleased to hear first-hand the actions that NHS Shetland, Rape Crisis Scotland and others are taking to address a lack of provision in island communities.
"Making this training more accessible and this new funding for doctors to become qualified to carry out these examinations will mean that victims should no longer have to travel to the mainland for evidence to be taken."
Earlier this year, an independent watchdog strongly criticised the way victims of sexual assaults in Scotland were treated by police and the NHS.
The inspector of constabulary (HMICS) said services offered to some victims were "unacceptable" and lagged behind the rest of the UK, with many victims being examined in police stations.
Funding to allow doctors in Shetland to pilot training for forensic medical examination services for victims of sexual crime has been announced.