Ministers announced yesterday that Linda McTavish has been appointed to lead the Lanarkshire board, while Janie McCusker takes the role at West Lothian.
However, the rest of the appointments - which include former First Minister Henry McLeish taking the helm of the Glasgow region - are male.
The Government's target in 2008 was to raise the percentage of applications received from women to 40%. But just 25% of the applications for the new roles as chairman or chairwoman of regional college boards were from women, despite females being well represented in college management.
Kezia Dugdale, education spokeswoman for the Scottish Labour Party, said the SNP had a "serious problem with women".
She said: "Whether it's appointing only two women to lead our colleges or failing to appoint more women to public positions more generally, the SNP just don't get it.
"Public appointments are important to ensure that organisations both reflect our community, but also ensure that those organisations are open and responsive to the diversity in our communities. On every count, the SNP are failing to ensure that women get a fair hearing and an equal standing."
Liam McArthur, education spokesman for the Scottish Liberal Democrats, added: "Ministers have repeatedly said they will seek to improve gender equality in government appointments. With women representing only two of 11 appointments it seems warm words are not being backed by effective action and ministers need to explain why."
Larry Flanagan, general secretary of the Educational Institute of Scotland, said: "In the week we celebrate International Women's Day it is disappointing to note that the appointments include only two women.
"Pursuing greater gender equality in all areas of the education sector should be a priority."
Stacey Devine, NUS Scotland women's officer, said: "Regional chairmen and chairwomen have a vital role to play in the running and direction of our colleges and it is vital they fully reflect the diversity of the colleges they serve.
"Equally, we know that this isn't something isolated to chairmen and chairwomen, and the wider membership of boards is often lacking in proper representation of women. The government and institutions should be getting round the table with women's groups and looking at how we can support more women to take up these opportunities."
A Scottish Government spokeswoman said the 12 posts had been advertised widely in national press and through social media.
"This was supported by targeted activity with organisations such as the Two Per Cent Club, Women on Boards and Women in Management Scotland.
She said: "The public appointment process is designed to support ministers to make appointments that reflect Scotland's diverse population through fair and open competition.
"The initial applications were about 75% male and 25% female and the appointed candidates broadly reflects this."
Education Secretary Michael Russell added: "I am confident that they are the right people to lead the sector as we look to develop a truly world class vocational education system."
The appointments have been made as part of a major restructuring of the further education sector, with the mergers of colleges along regional lines. Each region now has a board that will take strategic decisions over funding and provision in the region.
The regional chairman and chairwoman appointments were:
l Ken Milroy, Aberdeen and Aberdeenshire
l Willie Mackie, Ayrshire
l Anthony Jakimciw, the Borders
l Hugh Hall, Central
l Brian Johnstone, Dumfries and Galloway
l Ian McKay, Edinburgh
l Stephen Magee, Fife
l Henry McLeish, Glasgow
lLinda McTavish, Lanarkshire
l Keith McKellar, West
l Janie McCusker, West Lothian.
No suitable candidate was identified for the Tayside region.
As a result, this post will be held on an interim basis by David Sawers, a board member at Dundee and Angus college.