All practices should have received their first batch of swine flu vaccine by the end of this week and can then request additional supplies.
The order in which patients in the priority groups should be vaccinated is set out in the swine flu directed enhanced service (DES).
Patients aged six months to 65 years who are in clinical risk groups should be vaccinated first if possible, the DES makes clear.
Once this group is vaccinated, GPs should target pregnant women, then housebound contacts of immuno-compromised patients and finally over-65s in risk groups.
Experience of swine flu so far has suggested that pregnant women are at higher risk of serious consequences, the government has said.
The DoH and the Royal College of Obstetricians and Gynaecologists (RCOG) have developed guidance for assessing suspected swine flu in pregnant women.
Shortness of breath and high heart rate are indicators that a pregnant woman's condition may become serious, Sir Liam Donaldson, England's CMO said last week.
Practices can contact primary care organisations (PCOs) to order extra supplies of vaccines. But clinics should be arranged only once delivery dates have been confirmed, to avoid postponing or rearranging them, the DoH has said.
The amount of vaccine each PCO can order will depend on the size of its population and availability.
Ian Dalton, director of flu resilience for England has said that it is 'not acceptable for any practice to be uncertain of when their deliveries will arrive'.