A number of institutions - such as Aberdeen, Dundee and Edinburgh - even saw a worsening of their figures.
However, St Andrews University, which has been heavily criticised in the past for its record on improving participation, saw numbers from the poorest 40% of postcodes rise from 8.5% to 11.6%.
The institution with the best record was Glasgow Caledonian, where 33% of students are from the target postcode area.
Overall, 23.2% of students who began a degree in Scottish higher education in 2012/13 came from the 40% most deprived postcode areas compared with 22.5% in 2011/12.
Although the overall increase in poorer pupils represents just 0.7 percentage points, it comes before the full impact of recent Government policies on access have had time to take effect.
Drop-out rates, which have historically been some of the worst in the UK, also improved marginally, with 7.9% of students who began courses in 2011/12 leaving early compared to 8.9% the previous year.
Alasdair Allan, the Minister for Learning, welcomed the figures on access, but said he expected further progress in future years.
He said: "A record level of entrants from the most deprived areas of Scotland reflects well on our efforts to widen access and is something I expect to see more of."
However, the lack of progress was attacked by students groups and opposition politicians.
Gordon Maloney, president of NUS Scotland, said: "While any increase in the numbers of students coming from our most deprived communities should be welcome, the reality is that these figures show little progress on previous years.
"We know universities can't do it all on fair access, but they can, and must, do more than this. For all their warm words, many of our most elite institutions have stalled, if not gone backwards."
Kezia Dugdale, education spokeswoman for Scottish Labour, added: "The whole point of Scottish government legislation was to widen access to university places for young people in deprived areas - in fact the situation has worsened. The SNP Government has the worst record on widening access, the highest drop-out rates and the worst student support for the poorest students in any of the four home nations."
Dave Anderson, president of UCU Scotland, said any increase in students from non-traditional backgrounds was welcome, but there was "little cause for celebration".
He said: "Universities need to redouble their efforts both to widen access, but also to make sure, once there, that students receive appropriate support to prevent them from dropping out."
Alastair Sim, director of Universities Scotland, which represents university principals, said all institutions were "deeply committed" to widening access.
He said: "It's important to remember that this increase comes a year before the additional access places created by the Scottish Government come into effect. We can expect to see a step-change in next year's data.
"Widening access and retention go hand in hand. It's not enough to admit non-traditional students; they need to be supported to stay in and achieve successful outcomes, so it's very encouraging to see Scotland's continuation rate move in the right direction again for the fifth year in a row. This reflects a real concerted effort on the part of institutions in Scotland."