A hard core of academics is resisting attempts to recruit their help in vetting and monitoring foreign scientists.
Twenty-four students from "countries of concern" have been turned away by UK universities this year after the Foreign Office judged that they might use their expertise to make weapons of mass destruction.
Another undisclosed number have been deemed a "slight risk", and academics were asked to monitor their studies and restrict their access to some subjects. But many academics are boycotting the voluntary vetting scheme, which has the support of 95 institutions.
Ross Anderson, reader in security engineering at Cambridge University who led the successful fight against the export control bill, said most Oxbridge academics opposed vetting. He said that the Foreign Office was trying to discriminate against some nationalities without taking the blame by asking universities to reject applicants so that it did not have to refuse them a visa.
"The voluntary vetting scheme is unacceptable, and it is disgraceful that some universities have signed up," he said.
There has been a threefold rise in the number of cases referred for vetting since the September 11 terrorist atrocities, but a BBC investigation has found other examples of non-cooperation.
Sixteen of 41 microbiology departments responding to a survey by the File on 4 programme said they did not participate. Among the reasons given were a lack of confidence in the system and a belief that the process was "too bureaucratic and caused unnecessary delays".
The scheme began in 1994 after it emerged that some Iraqi scientists, including the head of the country's biological warfare programme, had trained in the UK. It targets postgraduate students from "countries of concern" - including Iraq, India, Pakistan, China and Israel - who apply to study a range of scientific and technical subjects.
In 2001-02, 612 applicants were put forward for screening.
Labour MP Andrew Mackinlay told the House of Commons foreign affairs committee last month that the voluntary nature of the scheme was "woefully inadequate" and called for it to be made compulsory.
He said rules should be drawn up with academe to allow inspectors to make spot checks on scientists' activities.
Patrick Lamb, deputy head of the Foreign Office's non-proliferation department, said: "The universities at an earlier stage were very intent and keen on maintaining academic freedom, although it is not necessarily the case now."
He said they were now wrestling with how to control access to sensitive work.