Health secretary Alan Johnson attended the launch of the first GP-led health centre in Bradford last week.
He congratulated Local Care Direct, the social enterprise that won the contract to run Hillside Bridge healthcare centre.
Mike Warburton, national director for the GP access programme, praised primary care trusts for procuring the centres in time for the Department of Health's target for a health centre in every PCT by 2009.
"For some PCTs, it's the first time they've undertaken such a procurement. To have everyone open in 2009 is a huge achievement," he said.
He acknowledged that a small number of PCTs would emerge from the procurement process without a chosen provider. These would be expected to re-advertise and award the contract next year, he said.
Mr Warburton admitted more could have been done to avoid the deluge of hostile publicity that surrounded the GP-led health centre initiative. He said the DH had not been prepared for the negative reaction because they saw the health centres as good news for patients.
The BMA mounted a campaign against the clinics in which patients signed petitions against the new centres at their own GP practices.
"We would want to get out a clearer positive message much earlier through a range of channels, and probably because we felt this was a positive advance, we didn't anticipate the BMA response which was probably the major driver of a lot of negative press coverage," Mr Warburton said. "I think we could have handled it more effectively."