Two in five people with a rare disease report difficulty getting a correct diagnosis, studies show.
A disease is classed as ‘rare' when it affects fewer than five in every 10,000 people.
But over 6,000 rare diseases affect around three million people in England, and inefficiencies in treating them are estimated to cost the NHS over £9m annually.
Speaking on Monday at the presentation of his 2009 annual report - his last before stepping down in May - Sir Liam Donaldson said improved training for GPs ‘would be helpful' to lower misdiagnosis.
‘It is understandable why diagnosis is difficult,' he said, pointing out that rare disease symptoms were often similar to those for common ailments.
He called for the appointment of a national clinical director for England and strengthened research to develop and market medicines for ‘orphaned' rare diseases.
Sir Liam's report identified a number of public health concerns. Physical inactivity ‘pervades the country,' he said, with 60-70% of adults not doing the recommended level of exercise per week.
This is despite the ‘substantial' benefits to health that physical activity can bring, Sir Liam said.
‘Being physically active is crucial to good health. If a medication existed that had a similar effect on preventing disease, it would be hailed as a miracle cure,' he said.
The report proposes new recommendations on minimum physical activity requirements in public health programmes, to be consistent across the UK.
Sir Liam also called for a new national cold weather healthcare programme to be developed, with healthcare providers asked to identify those at risk of harm from cold weather and refer them for assistance.
Sir Liam said he was pleased with several achievements during his time as CMO, particularly with regards to the public smoking ban.
However, he said he had ‘unfinished business' tackling the public health issues attached to the price of alcohol. Implementing a minimum alcohol price ‘will potentially make a huge difference and turn the tide on binge drinking', he said.