Mr Hunt was asked during health questions in the House of Commons on Tuesday if he would ask NHS England to ensure a fair deal for rural practices.
Anne McIntosh (Con, Thirsk, Malton and Filey) said NHS funding should reflect rurality, sparsity and age profile and the MPIG should be retained.
But Mr Hunt said the decision had been handed to NHS England and was out of ministers’ hands under the new structures.
GPs and senior politicians including foreign secretary William Hague, former Conservative party vice chairman Nigel Evans and Liberal Democrat president Tim Farron have warned practices could be forced to close when the MPIG top-up funding is withdrawn over seven years from 2014.
Earlier this month the prime minister said he would look carefully at the issue after Mr Evans warned of closures.
Mr Hunt told MPs he was meeting Yorkshire GPs this week to discuss the issue.
He said: ‘The most important thing about this very difficult issue about funding formulae is that it should be fair, and that is why in the new legislation we’ve given that decision to an independent body so that’s taken at arms length from ministers and that it makes the right balance between the issues of rurality, age and social deprivation.’
Under GMS contract changes imposed by the government in England, MPIG top-ups to core pay will be redistributed over seven years from 2014. About 65% of practices in England benefit from MPIG funding, with some receiving as much as half their core pay from the top-up.
GP reported earlier this year that the 100-patient Slaidburn practice could be forced to close just one year into the overhaul. The practice stands to lose £91,000 - a third of its total core pay and close to its entire annual profit - when MPIG is cut.
A significant number of practices across England could be in a similar position. The DH has estimated 100 practices in England could become unviable as MPIG is phased out.