Conservative Chris Chope questioned whether the government was right to attempt the merger of Inland Revenue and Customs and Excise IT systems when MPs are already inundated with complaints caused by the failure of the government to link the national insurance and Inland Revenue databases.
"They have not proved they have been able to succeed in doing that. And here they are, planning and indeed budgeting for job cuts on the basis that they are going to succeed in doing something much larger and more complicated," Chope said.
Liberal Democrat MP Vincent Cable said that experience in the private sector has already shown that merging two organisations with different cultures is difficult and often fails.
"Trying to achieve the double feat of managing IT and integrating two very different organisations could be beyond the government's capability," he said.
Although the departments have been working to reduce duplication of electronic information, a merger between the two departments will be difficult, a report by permanent secretary to the Treasury Gus O'Donnell. Records are still held in electronic "silos" in each department, with little cross-linking.
A merger between IT systems could prove more complex if the Inland Revenue's decision to replace EDS with Cap Gemini as its preferred supplier in the Aspire contract to modernise tax and national insurance systems next month runs into unexpected difficulties.
Bob Forthrop, chief executive of IT outsourcing consultancy Morgan Chambers, said it would be a major challenge for Customs and Excise and Inland Revenue to rationalise their IT systems while still providing a normal service.
"One of the biggest problems will be transferring data. It will mean having to do data cleansing. Having records of one person on the Inland Revenue and the same person on Customs and Excise and bringing them together is a major challenge," he said.
The new department could achieve some quick wins by rationalising basic infrastructure, such as desktops, telecoms and networks. But there are important questions to answer first.
Will the Inland Revenue or Customs and Excise systems take precedence? Will the government decide to mix and match? Which outsourcing supplier will win the business?
The Inland Revenue said no decisions would be made about merging IT systems until the appointment of a new management team. It said the Aspire contract would be no obstacle to a merger.