Universities urged to take account of new certificate
Michael Russell revealed he had discussions last week with university leaders, whom he described as very positive.
However, no university has made the baccalaureates, introduced last year, an entry requirement for any applicant so far.
University insiders warned it could take years for the new certificates to be become a standard part of applications.
Mr Russell said: "I am assured the universities will over a period of time will move to that.
"Certainly it's not happened in this round, but I would think in the coming year it would be a topic we will take forward."
He defended the new specialist qualifications as a success, despite only 108 pupils achieving one this year.
He said: "They are extremely important and have gone extremely well, and year on year they are going to build up.
"It will be my aim to keep talking to universities to make sure we get that happening; I see no reason why it shouldn't."
Figures from the Scottish Government show more than 200,000 was spent over the last two years promoting and developing the new qualification.
It comprises a selection of Highers and Advanced Highers plus a personal project, which the candidate chooses.
Mr Russell admitted: "It's going to be a slow burn, but there will be more next year."
Scottish Baccalaureates were a pledge in the SNP's 2007 election manifesto to encourage uptake of sciences and languages.
However, just 19 people achieved the language version this year.
A significant number dropped out, pupils claimed, after learning it would not be included in any offer from universities.
A spokesman for St Andrews University said it did recognise the individual Highers and Advanced Highers which make up the baccalaureate, but not the qualification as a whole.
He said: "We do not make offers based on the Scottish Baccalaureate."
A spokesman for Glasgow University said: "Consistent with all other Scottish universities, until it becomes a much more broadly recognised qualification undertaken by many schools, we will not use it as an entry criteria."
Des McNulty, Labour education spokesman, said: "A significant amount of money has been spent on these new qualifications and there are questions to be asked about value for money.
"Warm words are all very well, but hundreds of thousands of pounds have been spent and still very few schools are embarking on the Scottish Baccalaureate."
A spokesman for Universities Scotland said: "Universities are very positive about the baccalaureate, but at the moment still primarily admit on the basis of Higher results.
"That might change, but it is up to individual universities."
The Scottish Baccalaureate
SCOTTISH Baccalaureate awards are intended to stretch the brightest pupils and help improve transition to higher education.
They are obtained by studying a minimum of two Advanced Highers and one Higher in a range of subjects, plus a project of the candidate's choosing.
Science and language baccalaureates were introduced first and a social sciences version was expected to follow in 2011. Now the Scottish Government is waiting to see if uptake improves before any expansion.
The university admissions body Ucas awards the project element the equivalent of half an Advanced Higher, but it is still not formally recognised by universities.