The project, which begins this week, will include all types of employment and concentrate on issues involving women and race.
Last week The TES showed that women's chances of getting the top jobs were improving, but there was still a long way to go.
The Association of Colleges has already co-operated with unions in the sector to produce guidance on equal opportunities. Now a definitive picture of the current situation is needed, says Jocelyn Prudence, director of Employment at the AOC.
The recent Bett Report on Higher Education revealed substantial inequalities in the sector - 50 per cent of women are on fixed-term contracts compared to 38 per cent of men. Women are consistently paid less than their male counterparts.
David Triesman, general secretary of the Association of University Teachers, said: "Because academics have a vocation, it is no reason to subject them to this miserable exploitation." The report also revealed serious inequalities for ethnic-minority staff.
Queries on pay and conditions in FE brought to the Equal Opportunities Commission have raised fears that such a pattern may be repeated. The commission has called for a pay audit across a range of occupations as part of its three-year "valuing women" campaign, launched last October.
Under the EU part-time workers' directive which comes into force in April, employers will be obliged to ensure that part-timers receive the same employment rights as full-timers and are paid on a strictly pro-rata basis.
EOC commissioner, Janet Rubin, warned that this could have a significant effect on FE colleges. "If you don't monitor your workforce, you don't know whether you have got a problem or not," she told the the recent AOC conference of personnel managers.
So far there has been limited research. Concern has centred on how sex discrimination affects promotion prospects rather than pay so far.
However, a survey of 22 colleges by the Network of Women Managers in the same year revealed that although women made up 58 per cent of employees in the sample, they only hel 38 per cent of middle management and 31 per cent of senior management posts.
Sally Dicketts, the Milton Keynes College principal who chairs the network, believes that women may now be less inclined to apply for senior management jobs. Greater commercialisation and longer and less flexible hours can be a disincentive.
At the base of the pyramid, there are few statistics on lecturers. The new funding system introduced with college incorporation in 1992 depended on student recruitment and retention. Colleges had to keep close track of their clients but had less reason to monitor information on their staff. College independence and the use of short-term and part-time contracts mean that there is no consistent record of developments nationwide.
But there is anecdotal evidence of massive change throughout the sector. Workloads and contact hours have increased while administration time and the flexibility to manage time have diminished. Mergers have often been stressful and perceived as threatening. Beyond the core of permanent courses and staff, there is an expanding sector of short-term courses and projects.
These are more likely to receive money from sources other than the Further Education Funding Council and to use short-term and casual labour.
There is no firm evidence of sex discrimination at lecturer level, but with greater demands at work, employers' organisations and unions agree that some women do feel less able to take on full-time jobs. They are more likely than men to be carers, and may be forced by their circumstances into part-time contracts or working through agencies or third-party providers in disproportionate numbers.
Casualisation has raised many concerns for the unions. In some colleges blanket sacking of part-time staff has forced them to become agency workers. Self-employed staff have fewer benefits than permanent contract holders. For example, they will have to take out their own pension schemes. Agency workers may have low pay and "zero hours" contracts (where staff can be called in at any time to work) as many supermarkets and fast food outlets do. "The impact has been devastating," said NATFHE's assistant secretary for further education, Sue Berryman.