Tuition fees of up to pound;1,000 a year, levied on 60 per cent of students, did not appear to act as a deterrent, despite hostility to a controversial policy that is a central issue in the elections for the Scottish parliament.
The three main opposition parties want to abandon fees and may collectively be strong enough to force Labour to change course.
Throughout last year opposition politicians and many sections of the media condemned a policy they claimed would damage intakes. But figures now show the steady rise in the late 1990s continued in the current year.
The UCAS statement shows 31,952 students entered higher education, up from 31,447 the previous year and 30,599 the year before.
Some 3,500 students appear to have signed up for courses in the final weeks before the start of term, pushing the total above the previous year. The Scottish Office suggested up to a fifth of students enrol late.
Universities appear relaxed about the current fall in the number of applications from potential students, although the figures have been seized on to attack fees.
The latest UCAS statistics for the coming session reveal a 6 per cent fall in applications to Scottish universities by the end of March. At the same stage last year, applications were down by more than 4 per cent, provoking an outcry.
Ross Hayman, a UCAS spokesman, said there were 74,141 applications for Scottish places in 1998, a fall of more than 3,000 on the previous year.
"The total number of applications was down but places slightly up," he said.
The issue is complicated by multiple applications and each potential student can make up to six. Commenting on the current figures, Mr Hayman added: "At this stage, there is no need for concern and there are still far more applicants than places. Universities are not worried at all."
The UCAS national figures show applications from UK applicants aged under 21 are holding up, although the number of mature students is dropping, along with overseas applicants.