The call comes after UK researchers identified a rise in serotype one pneumococcal bacteria, which is not covered by the current vaccine.
Since September 2006, all under-twos in England and Wales have been given the vaccine, which protects against seven common pneumococcal strains.
Lead researcher Dr David Spencer, a consultant respiratory paediatrician in Newcastle, presented his research at the Royal College of Paediatrics annual conference in York earlier this week.
'Years ago, serotype one was not common in the UK,' he said. 'However, right now we are seeing an increase in the number of cases of the strain.
'Last year we saw 70 cases of serotype one at our Newcastle centre alone. It is estimated that there were around 800 to 1,000 cases in the UK last year.'
Introduction of the pneumococcal vaccine has probably led to the increase in serotype one, a pattern that has been seen in the US, said Dr Spencer.
'But overall it is important to remember the huge benefits that the vaccine has brought.
'In two years time there will be new pair of pneumococcal vaccines available that will include serotype one but until then GPs should be on the look out for signs of pneumonia in children.'
Dr George Kassianos, RCGP immunisation spokesman and Berkshire GP, said: 'GPs must remain vigilant for cases of pneumonia and meningitis.
'Although we have the pneumococcal vaccine, we can never relax as there will still be cases of disease out there.'