The college urged GPs with surplus vaccine to consider sharing supplies with practices who may be running out.
An RCGP statement said: ‘Colleagues are encouraged to share resources to liaise with local colleagues, or the PCT, and explore opportunities to make vaccine available in places where it is needed most.’
A DoH spokeswoman said: ‘We are aware of some reports of supply issues in some areas. We are working with the NHS at the local level to ensure available supplies of surplus vaccine are moved to where there is a need for them.'
However the department said there was not a national shortage of vaccine.
Ministers will also review the possibility of central purchasing of vaccine to ease the shortage.
The Health Protection Agency and the RCGP are both due to publish the latest figures on the outbreak later today.
The current seasonal flu outbreak would be classed as an epidemic if GP consultations passed 200 per 100,000 population.