Mr Mowat told the RCGP annual conference in Harrogate on Friday that new models of care he had seen since taking on responsibility for primary care in the DH were 'putting the GP in the driving seat in many cases', and driving better integration between social care, health and community services.
But he acknowledged concerns - raised by RCGP chair Dr Maureen Baker among others - that in many areas GPs were not being consulted as plans were being drawn up.
'In too many cases Maureen has said GPs are not being adequately consulted,' Mr Mowat said. 'Everybody is concerned in life about change.
'It is much harder to manage change than steady states - there is real difficulty in change. Change destabilises and can be seen as a threat.'
The government was expecting to see variation between STP areas in terms of the 'completeness' of proposals put forward, he admitted.
But in a challenge to the minister at the end of his speech, Dr Baker warned that in many STP areas GPs were not seeing the commitment to invest in general practice by 2020 that had been promised in the GP Forward View.
Mr Mowat said: 'STPs will not go forward if they are not right. It does seem to me to be very hard in an area if there is a consensus of GPs that has concerns about the STP to say that it is right.
'Particularly as one of the structural reasons we are doing this is to provide a tilt toward general practice. We just need to make sure that happens. It is important we have critical friends in that process.'
He said the government was trying hard to boost GP recruitment in line with its target to have an extra 5,000 GPs, telling the conference that general practice was 'the growth part of the NHS'.
Mr Mowat won applause for saying that controversial plans to to make the UK self-sufficient for doctors did not mean to 'devalue the foreign doctors and the fabulous contribution foreign doctors have made'.
He added that it was right that the government sought to put more UK students through medical schools. 'Our population is increasing, and it is right because we have a cohort of students, very often with straight As. And they find at the end of it all that they don't get into medical school - it is very hard to say to them why it is apparently government policy.'
Mr Mowat also conceded that the government hadn't done enough to retain older GPs in the workforce, pointing out that in other industries people would 'lose their jobs' for allowing a crisis to develop in which many older GPs planned to quit or have left the profession already.
He added the government needed to do more too to tackle the rising cost of indemnity, telling the conference: 'This is an issue that has affected you and your businesses. We would rather the NHS budget, which is tight, was spent on doctors not lawyers. At a structural level we need to be doing more as a government to make sure that specious claims do not happen and that stresses caused to you, people doing your best, are minimised.'
Full coverage of RCGP annual conference
Photo: Pete Hill