Problems combining multiple IT suppliers' services are partly to blame for bringing Government departments' computer systems to a "standstill", it is claimed.
The business and energy departments were the first to switch from a single computer system supplier to several under a Whitehall mandate to save money by procuring more IT services from SMBs.
But after cabinet ministers responsible for the divisions reportedly complained to the Prime Minister, an anonymous source close to the matter has now blamed the issues partly on problems of integrating different suppliers' services, each of which provide an aspect of the new computer system.
The source told CBR: "That's one of the issues. When you had one main contractor you had one person to talk to. The new model involves integrating a number of different contractors and suppliers, many of whom have not worked together before."
It added that it was "challenging" to bed down a complex range of hardware and software from different providers, though the departments are believed to be making progress now.
Business secretary Vince Cable and the energy department's Ed Davey complained to David Cameron that their IT systems were at a "standstill" a fortnight ago, since migrating from a Fujitsu-provided system in early May, according to the Financial Times.
While the Cabinet Office said each department is responsible for its own technology and services, CBR understands the new approach is mandated by Whitehall, and the departments admitted they were not aware how their suppliers were recruited.
An energy department spokeswoman said that while there were teething problems during the six-week migration, the IT system was now working well.
She said: "It was a big IT change and there was a bit of a perception of a few problems but it's working fine now. Everyone's emails and access to internet were fine throughout [the transition].
"It's quite a normal sort of thing to happen when you change IT systems when they're slow to start off with, but it's fine now and everything is much quicker and we haven't really noticed any problems for a few weeks."
Meanwhile the business department told CBR it was resolving intermittent problems it initially experienced.
A spokeswoman said: "This is an ambitious programme and we experienced some intermittent problems as a result of moving over to a new system. We are working hard to resolve them as quickly as possible and to minimise disruption.
"Much progress has now been made [and] lessons learned will help other departments when they renew their IT in the future."
The business and energy departments replaced a shared Fujitsu computer system provided under a 15-year contract worth £19m.
The new system, using several suppliers, is set to cut running costs by 40% over five years.
A Cabinet Office spokesman offered a robust defence of the project to use smaller suppliers, after recent figures showed central Government spending contributed 80% of a £191.5m total spend via G-Cloud since 2012.
"Civil servants need modern technology to do their jobs so we are replacing the expensive, inflexible and out-dated contracts which we inherited in 2010," he said. "Our Government IT reforms are saving taxpayers' money and ensuring SMBs can compete alongside bigger providers."
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