Michael Russell, the Education Secretary, told the Scottish Parliament the move would provide greater clarity on the issue.
The SNP also suggested the introduction of a university-style system of "clearing", which could match students with vacant places.
Last month, The Herald revealed colleges have waiting lists amounting to 21,280 applications.
The waiting list figures do not represent the total number of individual students involved because it is common to make more than one application.
There may also be cases where students have found a place at another college or returned to school, but remain on a list.
However, colleges, lecturing unions and student leaders believe the lists are evidence of unmet demand.
When the figure was released, John Henderson, chief executive of Scotland's Colleges, said demand for places was not always being met and colleges were having to turn people away.
Mr Russell initially dismissed the lists, but has now agreed to an official audit to find out how many students who applied to college could not get a place, as well as assessing how colleges keep waiting lists.
He said: "The Scottish Government is committed to tackling youth unemployment and every 16 to 19-year-old has a guaranteed offer of a place in training or education.
"Our colleges are also now focused on courses for young people that will improve their employability and deliver economic benefits.
"As part of this process, and of reforming post-16 education, we need to better understand the process of college applications.
"We must assess how individual institutions process potential students and how this impacts on others who have applied for a course."
Scotland's Colleges declined to comment, although some colleges contacted by The Herald privately welcomed the move.
One source said: "It is the first time we have had a recognition there is an issue here that needs to be looked at."
Larry Flanagan, general secretary of the Educational Institute of Scotland, which represents college lecturers, said: "While any steps taken to address long waiting lists for courses would be welcome, the most effective solution would be to widen access to educational opportunities by increasing investment in the further education sector and reversing the damaging cuts the sector has faced in recent years."
Robin Parker, president of NUS Scotland, called for quick action and added: "With youth unemployment, and unemployment more generally, at incredibly high levels, we shouldn't be turning people away from our colleges."
The money colleges get for teaching has been cut by nearly 16% between 2010/11 and 2012/13. It comes at a time when around one-quarter of 16 to 24-year-olds Scots are out of work.