Practices have also approached the RCGP about sharing vials between local surgeries to overcome isolated shortages in parts of the country.
Manufacturer Crucell voluntarily halted all deliveries of its vaccines to the UK while it investigates two batches on patient safety grounds.
GPs have contacted the DH about accessing the central emergency reserve of 400,000 doses, but the DH said it has yet to release any stocks from this reserve.
A DH spokesman said: 'As in previous years, once delivery of vaccine to general practice is underway the department builds a strategic reserve of around 400,000 doses of flu vaccine.
'This reserve is to use near the end of the seasonal flu vaccination programme if all other supplies have been exhausted.'
RCGP health protection lead Dr Maureen Baker said it was difficult to know how many practices would be affected by the withdrawal of Crucell deliveries.
RCGP immunisation lead Dr George Kassianos defended GPs' vaccine-ordering system following reports that practices in Gloucestershire had postponed 1,000 appointments.
He said: 'The vaccine-ordering system in place in England is excellent because it allows practices to order from multiple sources.'
'The central emergency reserve should come in with help to practices unable to source flu vaccines from any other source.'
The DH has asked practices to contact other suppliers in the first instance if they are experiencing problems. Local supplies of vaccines can also be shared between practices.
The department has been in contact with suppliers, which are working to secure more vaccine. Some suppliers have reported stocks are available for order.