The tobacco investment has come as a shock to many researchers, academics and staff, many of whom have spent their working lives searching for cancer cures.
George Butterworth, Cancer Research UK's tobacco policy manager, said: "The tobacco industry's deadly products are responsible for one in four cancer deaths.
"Many people would be shocked to learn that their pensions are invested in tobacco company shares - especially those striving to develop cures for diseases caused by this lethal industry.
"To help make it easier for organisations' pension schemes to opt out of tobacco shares, we're now funding the UK arm of Tobacco Free Portfolios to encourage investment funds to divest form tobacco stocks."
However, Universities UK defended its pension strategy.
"USS, as part of its investment duties, takes into account wider social, ethical, and environmental and governance issues, so long as that ensures that the assets of the scheme are invested in the best financial interest of members and their beneficiaries," said a spokesman.
"USS is also a responsible and engaged investor.
"They have for example, undertaken engagement with tobacco companies on marketing approaches and regulations around e-cigarettes."