The first phase of tendering closed last week, with the Department of Health announcing that 99 companies, including "all of the major national and international IT companies", had submitted expressions of interest to act as prime contractors for key parts of the project.
Richard Granger, director general of NHS IT, said, "This procurement represents a new way of working for the NHS. We are very pleased with the positive response from the IT industry."
However, as suppliers and health service users met this week in Harrogate for the HC2003 annual health informatics conference, it emerged that the first phase of the procurement has been surrounded by confusion.
While many specialist health IT providers responded to the tender notice, others held back, believing the Department of Health was only looking for industry giants, such as IBM and EDS, which would then construct their own consortia.
In a bid to clarify the process, the Department of Health issued a five-page questions-and-answers document on the procurement process on 12 March - just one day before the tender deadline.
The document showed that prospective suppliers have raised a series of fundamental questions, including whether the Department of Health wanted responses from prime contractors only, and what services would need to be provided to strategic health authorities.
Robert Morgan, chief executive at outsourcing advisory firm Morgan Chambers, said the current confusion could create problems later in the programme.
"Issuing an FAQ document just one day from the closing date of an invitation to tender could be symptomatic of a lack of preparation by the Department of Health, he said.
Anthony Miller, research manager at analyst group Ovum Holway, echoed these concerns. "Considering the size of the project, tenders of this size normally take a year and a half to sort out," he said.
"Trying to get these contracts moving fast is a noble cause, but one of my concerns is that we are beginning to see some warning signs of potential problems down the line."
Meanwhile, the chief executive of one of the UK's most successful and innovative small health IT companies was furious about the confusion surrounding the tendering process.
"Like most suppliers, we were not sure whether the official notice applied to us," he said. Then the Department of Health issued clarification when it was too late to do anything about it. Now we are left wondering whether we have missed the boat."
A spokesman for the Department of Health IT programme confirmed that there had been delays in issuing the Q&A tender document. "This was due to the need to ensure all the answers were properly approved. We are sorry if this caused problems but there have been no complaints from suppliers," he said.