The number of equivalent fulltime university and polytechnic students was flat compared to August 2017, while actual numbers decreased by 0.4 per cent, or 1174 fewer students - mostly from wanānga.
Industry Training Organisation enrolments increased by 0.5 per cent in Standard Training Measures, but actual numbers fell 1.2 per cent, or 1228 fewer learners.
This was mainly due to a 7 per cent decline in industry training enrolments compared to a year ago, offset by a 10 per cent increase in apprenticeships.
The Government praised the numbers as showing the policy was tracking well, but National has called the policy untargeted, middle-class welfare.
"There are 2400 fewer students in tertiary education and training than a year ago," National's tertiary education spokesperson Paula Bennett said.
"This expensive policy was designed to attract more students into tertiary education and it has completely failed."
But Education Minister Chris Hipkins said fees-free may be stabilising the previous decline in enrolments for level 3 and above courses, which fell by about 5000 in the year to the end of 2017.
"Given the difficult last couple of years that many of our polytechnics and institutes of technology have experienced, the stabilising of enrolment numbers in that sector is particularly encouraging.
"This has more than offset the large declines at several institutions, with an overall increase of 678 students on August 2017 figures."
He said that 31,600 fewer students borrowed to pay tertiary fees from January to September this year.
"The amount students had to borrow for fees also fell, down $193 million on the same time last year."
Europeans make up two-thirds of students in university and polytechnics, but this rises to 71 per cent for fees-free. For industry training, the increase is from 61 per cent across the sector to 79 per cent for fees-free.
Conversely, only 17 per cent of university and polytechnic students accessing fees-free are Māori, lower than the 20 per cent of Māori that make up all tertiary students.
The majority of university and polytechnic fees-free students were school-leavers; around 80 per cent were 19 or under, with a further 11 per cent aged 20 to 24. Fifty-nine per cent were female.
In industry training, 58 per cent of learners were aged 19 or under, with a further 18 per cent aged 20 to 24. Ninety-three per cent were male.
A briefing note from the Ministry of Education noted that the impact of fees-free "is expected to be limited" due to interest-free student loans, with increases most likely in the medium term as learners and providers adapt.
The Ministry of Education estimates that 50,200 people will benefit from fees-free support, including 4600 industry trainees, over the full 2018 calendar year.
Final year data for 2018 will be available in early 2019.