Ministers should not disguise policies based on their beliefs as being based on scientific evidence, the science and technology committee has said.
However, it is not convinced that this is the case, highlighting several incidents where policies were presented as if based on evidence when there was little or none available.
"We need to be able to feel confident that when government talks of 'evidence-based policy', this is backed up by sound scientific research. At present this does not always appear to be the case," said Phil Willis MP, chairman of the committee.
The committee's report,Scientific Advice, Risk and Evidence Based Policy Making, raises serious questions over the validity of the evidence behind several flagship programmes including Asbos, ID cards, Sure Start, and the decision to ban junk food in schools.
"Of course, not all policies need to be evidence-based and the committee recognises that political judgement is often exercised - but ministers should not disguise conviction-based policies as evidence-based," Mr Willis said.
"Where policies are strongly based on evidence, the scientific advice and evidence underpinning them should be published."
More worrying were accusations of "policy-based evidence making", which the committee's report claims could be seen as amounting to "scientific malpractice".
While the committee said it was not in a position to make a judgement on these claims, it adds "we have heard enough on an informal basis about the selective publication of research to harbour concerns".
"The overriding issue coming out of this report is that government does not have the capacity to evaluate the evidence coming out of government," Mr Willis told politics.co.uk.
The committee recommends that where the government describes a policy as evidence-based, it should make a statement on the department's view of the strength and nature of the evidence, and says such statements should be subject to quality assurance.
The committee also calls for a strengthening of the role of government scientific advisers, adding that this role should be split from the Head of the Office of Science and Innovation.
All future departmental chief scientific advisors should be external appointments who have occupied senior positions in their scientific communities and command the respect of their peers, the committee argue.