A DH report found that while the NHS was on course to meet its £20 billion efficiency savings target by 2015, PCTs stand to make even deeper cuts in the next six months than they have done so far in 2011.
Health secretary Andrew Lansley insisted the austerity drive 'does not mean cutting services'.
PCTs must average savings of £5bn per year by 2015 to meet the £20bn Quality, Innovation, Productivity and Prevention (QIPP) goal.
The report by the NHS deputy chief executive David Flory said PCTs had estimated they would save £5.9 billion from their spending in 2011/12.
Trusts have saved £2.5bn in the first six months of the year. But the rate of saving must increase further if the £5.9bn estimate is to be met.
The report, which covered the period July-September 2011, said: 'Whilst the NHS has reported a significant saving in the first six months of the financial year, it will need to continue with this focus, delivering further savings, whilst driving up quality, to achieve the forecast £3.4 billion savings in the second half of the year.'
Primary care is set for even deeper cuts. Of planned savings worth £214m in primary care, including dental, pharmacy and ophthalmic, just £97 have been made in the first six months of this year.
The report found further evidence of the squeeze occurring on GP referrals, as reported by GP in September when concerns were raised about the pressure on the profession to reduce use of diagnostic scans.
Mr Flory's report said: 'We have noted a reduction in GP written referrals into the acute sector, which is a positive indication of active GP engagement with QIPP and demonstrates a focus on referral practices to begin to shape service delivery for the future.'
The DH said quality of services had been maintained or improved despite the cuts. MRSA and C. difficile infections in hospital settings continued to fall, at 33% and 16% lower respectively than the same period in 2010.
On announcing the report, Mr Flory said: 'The NHS is in the early stages of its plans to deliver up to £20bn of efficiency savings by 2014/15 whilst maintaining or improving quality. The results from the second quarter of 2011/12 are encouraging, showing the NHS continues to deliver strongly for patients while maintaining a healthy financial position.'
Health secretary Andrew Lansley said: 'We know that despite the increase in funding, the NHS needs to save up to £20 billion from within its budget to meet these future challenges. Where the NHS can do things better and save money to reinvest in patient care, it must do so.'
He added: 'We are absolutely clear that this does not mean cutting services - this means getting better value for every pound spent in the NHS so that it can continue to improve and deliver better services for patients every day.'