She told a King's Fund conference on alternative primary care providers, in London, that the DoH will press the BMA for an end to the top-up system.
Ms Hewitt cited a PCT which said its deficit was in part due to paying the MPIG correction factor to practices with falling patient numbers.
'One PCT I spoke to was dissatisfied with its older GPs who were operating out of unsatisfactory buildings, so they opened their own centre with salaried GPs,' she said. 'There was a big transfer of patients but the PCT was hit by double costs not least because of the MPIG.'
The health secretary's comments came as a GP survey found that three quarters of LMC representatives believed that any proposal to reduce the value of the MPIG should be opposed.
A fifth wanted proposals to reduce reliance on the MPIG, but many said that this would need to be done in line with other changes. One respondent said he would only support MPIG reductions when it was replaced by a proper global sum.
The survey was carried out among representatives at last week's annual LMCs conference in London.
GPC chairman Dr Hamish Meldrum told the LMCs conference that there might be more pressure to scrap MPIG but he 'had heard this umpteen times from the government', and other issues had to be addressed first.
'People forget why we had MPIG in the first place,' he said. 'It's because money was raided from the global sum. Unless that changes we just ain't going to agree to change MPIG.'
Philip Grant, a member of the NHS Employers GMS negotiating team said: 'It has been agreed with the GPC that future uplifts to the global sum should seek to reduce the reliance upon the correction factor. This is in response to an increasing recognition that MPIG prevents equitable distribution of global sum resources.
'However, we have not discussed the timescale over which any changes might take place.'
Ms Hewitt's words follow the DoH's recent White Paper, which stated that it would 'ask NHS Employers to consider MPIG and its impact on equity when discussing incentives for 2007/8 and beyond'.
LMC representatives called for the introduction of a global sum that did not depend on a correction factor, but until that happened, they mandated the GPC to ensure that MPIG was inflation-proofed and that MPIG-style protection was built into all new GMS contracts.