A coalition row has erupted after Lib Dem minister Vince Cable was reported to have called the Tories' flagship IT policy "shambolic".
According to the Financial Times, Vince Cable and Ed Davey complained to David Cameron over slow emails and other IT problems at their departments.
They are said to have blamed Tory Cabinet Office Minister Francis Maude's IT procurement policy.
The Cabinet Office said the ministers' own departments were to blame.
Business Secretary Mr Cable and Energy and Climate Change Secretary Mr Davey are said to be angry about slow and intermittent emails and network problems at their departments since they started migrating to new systems in May.
The problems are said to have nearly brought their two departments to a standstill.
'Messed up'
The departments share an IT system, which was previously provided by Japanese computer giant Fujitsu under a 15-year PFI deal worth £19m a year.
Under new Whitehall procurement procedures, they are using several different suppliers on shorter contracts.
The business department is suffering IT problems Francis Maude is attempting to end the dominance of IT giants at Whitehall - and hand a bigger share of contracts to small and medium sized companies (SMEs).
Mr Cable is reported to have called for a halt to the initiative - one of the Conservative Party's flagship policies to boost entrepreneurship - until lessons have been learned.
But Cabinet Office sources suggested the energy and business departments had "messed up" the procurement of the new contracts and were trying to shift the blame to Mr Maude's team.
'Outdated contracts'
A Conservative government source told BBC News: "It is rather strange that the secretary of state for business seems to be against small business."
Mr Maude's officials have pointed out that the new IT system at the two departments is not, in fact, being provided by small companies.
They say officials are taking time to get used to new ways of working, with several contractors handling IT instead of one big supplier. They also point out that the new IT contracts at the two departments are 40% cheaper.
A Cabinet Office spokesman said: "Civil servants need modern technology to do their jobs so we are replacing the expensive, inflexible and outdated contracts which we inherited in 2010.
"Our government IT reforms are saving taxpayers' money and ensuring SMEs can compete alongside bigger providers.
"Departments remain responsible for their own technology and services."
Mr Cable's office has been contacted for a comment.
James Potter