Premature baby charity Bliss made the claim after asking 21 neonatal networks how they are spending a £72m cash boost over three years.
Only a third of the £20m allocated in the first year (2003-4) was spent on improving neonatal services, it said.
But the Department of Health insisted neonatal care was improving.
The charity's research found that of the extra cash earmarked for premature baby care nationally - a third had resulted in no improvement.
This had either been spent on maintaining existing nursing and care costs or was lost plugging holes in primary care trust budgets not related to neonatal care.
One network had spent much of the money on cardiology services, Bliss said.
And many of the 21 neonatal networks could not say how they were spending last year's money.
At the end of two year's of funding, the research showed, only 29 extra cots had been introduced, compared with the 200 or 300 that were promised over the three years by the government.
As a result sick babies are still having to be transferred long distances for appropriate intensive care services.
A Bliss spokeswoman said it welcomed the extra funding for the care of sick and premature babies but that it was "unacceptable" that much of it had not been spent on the services it was meant for.
"We must ensure that the monies given to them to develop neonatal services are used for this purpose."
The government should have ring-fenced the money, she said, adding that it should not be down to individual primary care trusts to be responsible for tackling a crisis of national proportions.
She also said that neonatal networks needed around £75m a year to bring them up to the standards recommended by the British Association of Perinatal Medicine.
Critically ill infants were still not given the level of care provided in paediatric or adult intensive care, she added.
The Bliss claims were given some credence by doctors in Yorkshire who warned in April 2004 that staff shortages and a lack of specialist cots are putting some infants at risk.
But the Department of Health said that neonatal intensive care services were improving but acknowledged there was more work to do.
A Department of Health spokeswoman said: "We will be discussing with network managers the way forward and how to improve further.
"The DoH has provided extra funding of £20 million per year to improve services and this has gone towards setting up neonatal networks, providing additional cots and securing rapid access to highly specialised intensive care for the most vulnerable.
"It is necessary to look at overall trends rather than the results of one year, and overall we have the lowest ever recorded infant mortality rate."
The department pointed to national statistics that showed mortality rates had declined among the most vulnerable.