This could have far-reaching implications for salary levels, and comes as local government is already under severe financial pressure from equal pay claims.
Citing the Sex Discrimination Act, the commission intends to find out whether classroom assistants in primaries are undervalued because they are seen as having traditional "female" skills.
It is concerned that no account has been taken of the development of classroom assistants' roles. "In particular, there appears to be no recognition of the skills and responsibilities used in supporting early-years learning and no opportunities for career progression in this area," a spokesman for the commission said.
The investigation, lasting about a year, will be seen as timely since the use of classroom assistants is being included by the Scottish Executive in the pound;1.2 billion savings it has to deliver by 2007-08.
The executive's education department has estimated that employing classroom assistants has led to savings of pound;44 million.
There are approximately 7,500 classroom assistants in primary schools in Scotland, 98 per cent of them women. The EOC found that the rate female assistants are paid varies across local authorities, with annual pro-rata salaries ranging from pound;5,395 to pound;9,588. Hourly rates range from the minimum wage of pound;5.05 to pound;8.93.
John Wilkes, director of EOC Scotland, told The TESS: "This investigation offers a unique opportunity to examine the undervaluing of traditional 'female' skills, such as those related to caring and domestic roles.
"Many will be shocked by the low levels of pay, some just reaching the minimum wage at pound;5.05, considering the wide range of tasks, skills and experiences."
Mr Wilkes added: "We fully recognise the distinction between classroom assistant and teacher roles. However, we have concerns about whether the current system gives proper consideration to the range of 'non-teaching'
support for learning tasks performed by classroom assistants."
One initial step in the investigation will be to survey teachers and headteachers for their views.
A spokesman for the EOC said he hoped the investigation would identify the full range of tasks performed by assistants and establish their range of skills.
The EOC has already commissioned preliminary research by the Scottish Centre for Employment Research (SCER). It found there was "a lack of clarity" about the work done by classroom assistants to support learning.
Classroom assistants were introduced in 1998 under a pilot programme designed to raise pupil attainment levels by freeing teachers' time to teach, assisting in the supervision of pupils, and providing support for learning under the direction of teachers.
However, since then, they have been given more responsibility for planning and participating in support for pupils' learning.
SCER found teachers and parents supportive of their contribution but added:
"Teachers and heads are still uncertain about whether classroom assistants have the skills and knowledge adequately to support pupils' learning. There was a real desire to see more formal training provided."
Classroom assistants are not meant to progress from administrative tasks to supporting learning unless they have undertaken the personal development award, which is not universally available.
Greg Dempster, general secretary of the Association of Head Teachers in Scotland, said: "Obviously, the gender issue is one which affects teachers as well as classroom assistants in that the proportion of women in primary is massive in comparison to men."
A Cosla spokesman said: "Classroom assistant posts are very popular and anything that can be done to improve the experience of such positions further will be considered."