The report recommends a revised set of QOF indicators and payments to reward GPs who target their most at-risk and impoverished patients.
Evaluating attempts since 1997 to reduce health inequalities across England, the report says the DoH was slow to implement effective projects.
Trusts only started to make progress in 2006, leaving Labour's target of cutting inequalities by 10 per cent by 2010 unachievable.
The NAO claims improvement in the treatment of many diseases has 'slowed markedly' because most GPs now achieve close to maximum QOF points.
'GPs can achieve full payment ... without covering the entire practice population and as a result the hardest to reach and most in need groups may not be helped,' says the report.
But GPC deputy chairman Dr Richard Vautrey said: 'People misunderstand the difference between the payment systems of QOF and the work we do with each patient.
'Some people want to see GPs with more of a public health role. We do our best to meet the needs of the patient in front of us, and are mindful of the needs of those in the community, but we are already working hard with constrained resources.'
The report calls for NHS health checks to focus on high-risk patients, not the whole population. Darzi centres have not fully tackled doctor shortages in deprived areas, it adds.
Increasing access to BP and cholesterol-lowering drugs and smoking cessation services are noted as key cost effective ways to boost health in deprived areas.
Life expectancy has risen since 1997, but the gap between rich and poor continues to grow. Those in the poorest areas die on average 10 years earlier than those in the wealthiest.