The aim of the new flu service, which will include a hotline and internet advice, is to help relieve the pressure on frontline NHS staff.
Other parts of the UK may join the service at a later stage if they feel the need.
GPs, although warning it needed to be well funded, welcomed the FluLine phone and internet advice.
But the Lib Dems say documents obtained under the Freedom of Information Act reveal that the Treasury was expected to approve the scheme in June last year, but did not do so until December.
A number of email exchanges between the Treasury and the Department of Health showed discussions of costs and timings, the party said.
Not only is this putting an additional burden on GPs, but the government is having to use tax-payers' money to cover the cost of setting up an interim service
Lib Dem health spokesman Norman Lamb said "Whitehall in-fighting" meant GPs were having to cope with "a large number of calls that should have been directed to a national FluLine".
"It is incredibly frustrating that the national flu strategy is inevitably being undermined because this central plank is not in place," he said.
"Not only is this putting an additional burden on GPs, but the government is having to use taxpayers' money to cover the cost of setting up an interim service which should not have been necessary in the first place."
Responding to the criticism, a Department of Health spokesman said the scale of the flu service project meant it needed to be "rigorously tested".
"Launching without this could risk wasting taxpayers' money," he said.
The government has tried to clear up confusion over mothers-to-be advice
"Subject to final checks, the first release of the system will be in place at the end of this week and will further ensure the NHS is well placed to respond."
The health secretary earlier confirmed: "The flu service will be able to quickly diagnose people with swine flu and give them the opportunity to get anti-virals from local centres, meaning in turn that GPs' time will be freed up enabling them to deal with other illnesses," he said.
Mr Burnham stressed that swine flu had proved to be a mild virus in the vast majority of people.
"We are asking the NHS to pick up the extra pressure, but nothing has changed, and, as the World Health Organization has acknowledged, this country has some of the best plans to deal with it in the world.
"We couldn't be in a stronger position."
Twenty-nine people have now died in the UK after contracting swine flu - 26 in England and three in Scotland.
The government has warned that the number of deaths from the virus this winter in the UK could reach between 19,000 and 65,000.
However, during the 1999 to 2000 winter, seasonal flu deaths reached 21,000 and even during average winters there are normally anywhere between 6,000 to 8,000 deaths.
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