Speaking at a media briefing in London on Thursday, Ian Dalton said that GPs and practice managers had made 'really good progress' with the vaccination plans.
Mr Dalton said that the remaining third of PCTs that are still to finalise arrangements were very close to doing so.
Professor David Salisbury, head of immunisation at the DoH, added that the vaccination programme for healthcare workers was going well with 343,000 doses administered so far.
'We have given out three times as many doses to healthcare workers as we did for the seasonal flu jab last year.
'We have also vaccinated 101,000 pregnant women and three million patients in the priority groups. This data comes in arrears so we hope to see it increase further.'
The latest figures on vaccine uptake come as the pandemic shows further signs of slowing down.
In England, there were 9,000 new infections last week down from 11,000 the week before, while in Scotland the number of cases has fallen under 8,000. Cases are also on the decline in Wales and Northern Ireland.