Mike Russell also described figures which show that 70,000 people have been cut from college rolls in the last two years as an "inappropriate way to measure student numbers".
A survey of 36 colleges by sector representatives Colleges Scotland in October last year suggested that over 21,000 applicants are on college waiting lists.
That same month, the Scottish Government said that 70,000 people had been cut from the college headcount in Scotland in the preceding two years.
The Education Secretary faced sustained questioning on college places from Labour MSPs at Holyrood.
Mr Russell responded with an attack on Labour's u-turn on university tuition fees.
He also urged the opposition to observe "a period of silence" until official waiting times figures are published.
Labour MSP Neil Findlay said places for students with learning disabilities were cut by 34% last year, and asked what the proportion will be this year.
Mr Russell said: "Providing we work with the sector and we show our intention to work with the sector, and the sector is working with us, then clearly we will also be able to put this matter into outcome agreements, and we look forward."
Labour MSP Ken Macintosh asked how many college places for over-25s have been lost in the last three years by headcount.
Mr Russell said: "I have made it clear on many occasions that headcount is an inappropriate way to measure student numbers, whatever the age group, in a sector which is predominantly part-time and where courses vary so widely in length.
"Headcount is a blunt measure. It gives no indication of the economic relevance of a course or the level of teaching resource which the college decides it's appropriate to apply.
"The way to make meaningful comparisons between years is using the measure of full-time equivalent places, by which it is clear that under this government college places are being maintained."
Mr Macintosh said: "I'm surprised the minister doesn't recognise that there is a place for headcount given that these are the numbers of real people actually going to college and benefiting from a college education."
Labour MSP Mark Griffin urged the Scottish Government to publish official college waiting list figures as soon as possible.
Mr Russell said the publication is "keenly anticipated" but advised Labour MSPs that it "should not anticipate it with enthusiasm given the things that they have said in the past".
SNP MSP George Adam said: "The in-term results of the audit of college waiting lists across Scotland has already shown that claims of 21,000 individuals on college waiting lists are actually false."
Mr Russell said: "That is indeed true. I would have thought, in the words of Clement Atlee, a period of silence would be in order."
SNP MSP Fiona McLeod faced groans from Labour when she described the party's policy review which could see Labour back university tuition fees, as a "cuts commission".
Mr Russell said: "Labour members are now groaning when they hear about the cuts commission. If they convert that groan into opposition over some of the things that are proposed then clearly we are going to have a better society in Scotland.
"Perhaps that will also lead them away from the enormous mistake they made last week when they abstained on free education in Scotland.
"Labour made the promise: We won't introduce upfront or backdoor tuition fees.
"I find it astonishing that a group of people who signed a pledge on that merely two years ago couldn't actually vote for it when it came to this chamber. Oh dear. They should groan at that too."