Students on physics or engineering courses often struggle to work with symbols, solve equations or even add fractions.
Universities blame weak curricula and teacher shortages and are introducing their own programmes to tackle the problem.
A "virtual support centre", known as MathsCentre, for students who find maths difficult, is being set up by the Learning and Teaching Support Network.
The network is also distributing information on diagnostic tests used to assess students' maths when they arrive, as well as methods of tackling problems such as learning support centres and summer schools. Some universities are introducing streaming for first-year students or extending courses to four years.
One of the scheme's co-ordinators, Pam Bishop, of the school of mathematics and statistics at Birmingham University, said pupils were discouraged from doing maths A-level by the perception that it is difficult. She said league-table pressures meant some schools were entering pupils for intermediate-level maths GCSE to ensure success. "But this is not necessarily better for the children. You can get a pass at intermediate level without doing any algebra," she said.
The result is that students end up on physics and engineering degrees who have done maths only to intermediate GCSE and cannot tackle basic algebra, let alone the logarithms and calculus demanded by the courses.
Tony Croft, director of the mathematics education centre at Loughborough University, said the falling popularity of science degrees forced universities to admit students they would not have considered 10 years ago, meaning some arrived with limited maths skills.
"In some schools there are not enough maths teachers," he said. "There is also an issue around the curriculum and how basic algebraic skills are developed by the GCSE at intermediate level. We are talking about the ability to add fractions, work with symbols, solve equations and rearrange formulas."