The report, entitled Behind Closed Doors, claims that the average level of military funding of UK universities is up to five times larger than government figures suggest.
The most recent government figure for military funding of British universities is £44m in 2004.
The report says that since 2002, new military research groups that are supported by publicly-funded research councils, military corporations and the ministry of defence (MoD) have surfaced in many universities.
The UK is the world's third biggest spender on military research and development, receiving $5bn net expenditure from the ministry of defence alone in 2005 to 2006.
Langley said the growing influence is reflective of how universities in the UK are becomming increasingly commercialised.
"If you're undertaking research, and receiving commercial funding for it, you're expected to produce results which have a short-term economic goal.
"Whereas if you're funded by a research group which is not tied to an agenda then you're more likely to be motivated by scholarships and interest."
Langley, an independent scientific consultant, said research students today are "largely" funded by commercial organsiations, particularly in the areas of science and engineering.
He said staff in universities were worried about the power of vested interests, especially large corporations, in influencing the research agenda and making it more "conformist".
Corporations that are known to develop military technology and provide funding to UK universities include BAE Systems, Boeing, GKN, General Dynamics, Lockheed Martin, QinetiQ and Rolls Royce.
The rising involvement of such companies means that high-technology, weapons-based approaches are given priority over political or diplomatic methods, said Langley.
"The staff we spoke to were not prepared to go public with this, they felt very uncomfortable," he said.
"Individual resarchers wouldn't raise their voices against this – they're caught between the universities and their funders."
Universities denied the military was playing a greater role in research agendas.
Professor Rick Trainor, president of Universities UK, a higher edication action group, said: "We do not accept the claim that universities are insufficiently accountable.
"Higher education institutions must account for their use of funds from a range of public and private sources.
"Most institutions will have frameworks in place that govern the process for accepting funding, particularly from commercial sources, and identifying and dealing with potential conflicts of interest."
Ensuring transparency should be a key part of an institution's corporate responsibilities, Trainor said, "though on occasion there will of course be legitimate commercial or security reasons for restricting information on some activities.
"Where this is the case it should, however, be clearly stated."
A spokesman for the MoD said it was aware of its level of investment with universities "when there is a direct contractual agreement".
"The MoD offers contracts for specific services and products and so the level of spend with individual universities and departments will vary widely between organisations and over time," he said.
"Individual project teams are aware of the sources of subcontracted information, services and components for their areas of responsibility.
"However, all subcontract details are not gathered centrally. The MoD does not believe that the such information is of either practical use or its compilation represents value for money for the UK tax payer."