A Midland academic has led calls accusing the Home Office of distorting its research for the Government's political ends.
Another criminologist has also called on academics to b oycott the department because of its "biased agenda".
The Home Office spends £20 million on research papers each year, which are supposed to offer independent analysis of subjects such as crime and asylum, so that appropriate policy can be drawn up in response.
This month's edition of the academic journal Criminal Justice Matters accused the department's research programme of "rubber-stamping the political priorities of the day".
In one paper, criminology professor Tim Hope, from Keele University in Staffordshire, revealed that research he carried out into an anti-burglary project showed it would have actually increased the crime by two-fifths.
This result was "something of an embarrassment" to the Home Office, which never publicly commented on it and did not select the findings for a full report, said Prof Hope.
"It was with great sadness and regret that I saw our work ill-used and our faith in government's use of evidence traduced," he said.
The Home Office commissioned further research on the same anti-burglary scheme - which focused on making homes more secure - and analysed it using different techniques.
"Through various manipulations of the data, the Home Office method does what it can to capitalise on chance, producing much more favourable findings overall," said Prof Hope. But for individual projects, the method produces considerable distortion."
Prof Hope said the anti-burglary scheme he studied in 2004 would have led to a 39 per cent increase in home break-ins, although its negative impact was moderated by other factors in the study area.
"Rather embarrassingly, the efforts of (the project) appear to have offset an otherwise generally favourable burglary reduction trend," he concluded.
Also writing in the journal, published by the Centre for Crime and Justice Studies at King's College London, Reece Walters, of Stirling University, called on academics to boycott participation in Home Office research.
He said: "It is clear that the Home Office is only interested in rubber-stamping the political priorities of the government of the day.
"To participate in Home Office research is to endorse a biased agenda that omits topics of national and global concern in favour of regulating the poor and the powerless.
"I say academics must boycott the seeking of, and participation in, Home Office research."
A third article in the magazine said an influential study which is influencing millions of pounds of public spending was "flawed".
Chartered statistician Paul Marchant, of Leeds Metropolitan University, criticised a 2002 Home Office report which concluded that better street lighting led to reduced crime.
"My ongoing debate with the authors and the government body involved is that the use of statistical methods in this study lacks sufficient rigour and so the claim is not supported by the data," he said.
"This is more than a matter of academic interest, as policy decisions cost potentially billions of pounds."
Acting director of the Centre for Crime and Justice Studies, Richard Garside, said: "At a time when the Government's claims on crime and crime
reduction are facing increased scrutiny, this issue of Criminal Justice Matters is a timely contribution to an important debate about the way that research is conducted and its results understood.
"It is important to look behind the spin, claim and counter-claim that so often seems to bedevil public debate about crime, its causes and solutions."
Home Secretary Charles Clarke has appointed a cross-party panel to come up with proposals for a complete over-haul of crime statistics in England and Wales, after acknowledging that they were no longer trusted by the public.