The Educational Institute of Scotland (EIS) said official figures showed numbers had dropped by more than 12% between 2010 and 2011 – from 357,729 to 314,585.
The union blamed Scottish Government cuts for the fall in numbers, which follow a sharp decline in the number of lecturing staff.
The row blew up as lecturers held a rally at the Scottish Parliament in protest at continuing cuts to further education.
Larry Flanagan, general secretary of the EIS, said: "The sharp decline in student numbers across Scotland's further education sector shows that continuing cuts to college funding are damaging educational opportunities across Scotland."
A Scottish Government spokesman said: "The figures in the EIS news release relate to 2009-10 and 2010-11, and reflect the fact that, in line with Government expectations, colleges prioritised full-time courses – in particular for young people at risk of unemployment – and placed a lower emphasis on part-time courses not focused on employability."