The report of 26,427 people who started a modern apprenticeship in 2011-12, only 74 (0.3%) were disabled or had learning difficulties.
While 43% of the new starts were women this compared unfavourably with England, Wales and Northern Ireland.
The EHRC said gendered segregation in apprenticeships is still "unacceptably high", as only 2% of engineering or construction placements went to women in 2011-12.
The report also found less than 2% of all apprenticeships in Scotland are offered to ethnic minorities.
Missing a trick
EHRC director in Scotland Alastair Pringle said the Scottish Government is "missing a trick" by failing to maximise the potential of the Scottish population.
"We believe the Government needs to demand greater effort from their contractors to drive up the representation of ethnic minorities and disabled people and to open up occupations which have traditionally been 'men only' to young women," Pringle said.
The report found although men are increasingly moving into traditionally female apprenticeship programmes, there is no evidence of women moving into traditionally male schemes.
"It is disappointing to see that the profile of apprenticeship opportunities is a very old one, men doing the 'heavy work' like building and women doing the 'softer work' like caring and teaching; and disabled people not having much work at all," said Pringle.
"If we are to emerge from the recession successfully, we need to harness the talents of all of Scotland's people."