Ministers have also announced plans to adjust the tariff for NHS services, allowing GP consortia to drive down the cost of buying these services.
Jim Easton, England's national director for improvement and efficiency, spoke about the changes at the NHS Alliance conference in Bournemouth last week.
He said the DoH was trying to find the right balance between not saddling consortia with PCT debts and not pretending such legacies do not exist.
He said government thinking was going in GPs' favour. 'The secretary of state is deeply minded about giving you best start he can,' he said. 'The wind is going in your direction.'
But he also said GPs should share some responsibility for the creation of the debts.
'Some of them, you might feel, were completely out of your control' he said. 'But some of them are related to behaviours going on in your part of the world and it would be wrong to pretend that's not the case.'
Health minister Lord Howe acknowledged at the conference many GPs' concerns that consortia may inherit debts.
But he said: 'We are working with SHAs to straighten this out and we will be saying more about this in the new operating framework when it comes out later this year.'
Lord Howe also announced that economic regulator Monitor will set maximum tariffs for NHS services in the future to drive up competition and productivity.
Dr David Jenner, PMS/GMS lead at the NHS Alliance, said the move would allow PCTs and GP consortia to budget better and control costs.
'In areas with one large provider PCTs and GP consortia could feasibly negotiate a discount for bulk,' he said.
Mr Easton also said the tariff is set to be reformed to incentivise service provision in primary care.