The NHS Information Centre report found that medicines in six treatment areas were prescribed at rates lower than would be expected for the disease prevalence. All had been backed by NICE as good value for money.
The Association of the British Pharmaceutical Industry (ABPI) said this showed certain drugs are 'underused' by the NHS, and that the picture had worsened since 2010.
In November 2011, a GP investigation found GPs had been barred from prescribing drugs recommended by NICE because PCTs had chosen to 'blacklist' certain treatments to cut costs.
In September 2012, a GP survey found one third of GPs said PCTs were still ignoring a government order not to ration treatments on the basis of costs alone.
The report, Use of NICE-appraised medicines in the NHS in England, in 2010 and 2011, looked at the NHS's use of 52 medicines across 25 treatment types. These had been approved by NICE in 35 technology appraisals.
In the analysis, only 13 treatment types were considered due to difficulties comparing observed with predicted use.
The report's authors calculated the expected total 'defined daily dose' - a standardised measure of treatment volume - based on incidence of the indication. They compared this with observed use of drugs using NHS prescription data.
Six medicines were used more frequently and six less frequently than expected, with mixed findings for one drug, the monoclonal antibody ranibzumab.
Figures suggest the NHS provides around 2,312 fewer courses of breast cancer drug trastuzumab than expected.
Use of treatments for acute coronary syndromes was down 20% on the level expected from incidence of the disease.
Motor neurone drug riluzole was used 38% less than anticipated, and drug misuse treatment naltrexone was prescribed 12% less than expected.
Meanwhile, statins were used by the NHS almost two-and-a-half times more frequently than expected.
Drugs for osteoporosis were used 28% more than anticipated, with varenicline for smoking cessation used 17% more than expected.
Use of insulin glargine and determir fell from 15% greater use than expected in 2010 to 7% more in 2011.
The report stressed that the findings did not necessarily show that these drugs had been 'over' or 'under' prescribed.
The report said: 'Clinical judgment, the time taken for the population to present to services to enable changes in prescribing, and demographic differences across healthcare economies are potential explanations for variation in results.'
Many treatments were excluded from the analysis, including those primarily used in children, those which are formulated as creams, ointments, foams or gels due to dosing issues.
The report admitted that it had to predict drug use because 'data on the number of patients diagnosed with specific conditions or being treated is not collected centrally by the NHS'.
Stephen Whitehead, ABPI chief executive, said: 'It is vital that we understand when NICE-recommended medicines are not reaching patients. This year's report shows that many medicines, including new medicines, still continue to be underused.
'It is also clear that there is too much unwarranted regional variation - so in some parts of the country people can access a medicine, whereas just a few miles away, another person can't.'
He said the issues must be addressed 'as a matter of urgency'.