The service, based on the Maze site in Lisburn, will operate with a doctor and paramedic on board from the outset.
The campaign for the helicopter emergency medical service (HEMS) was begun by the late Dr John Hinds.
Northern Ireland was previously the only area in the UK without such a service.
The launch of the service has been the subject of some uncertainty, and the announcement that it would be doctor-led follows an intervention by emergency medics.
"This will deliver the maximum benefit to patients through the triage and treatment they can jointly provide at the scene before onward transfer to the most appropriate hospital," the department said.
"The ambulance service can now proceed with the recruitment and training of these staff.
"The Belfast Trust can now proceed with enabling works to the Royal Victoria Hospital helipad which should take approximately nine months to complete, however the service can commence in the meantime by landing at alternative sites nearby (i.e. Musgrave Park Hospital).
"However, the most important thing is the medical intervention by a doctor and paramedic at the scene of the incident which makes the key difference to saving lives."
Last year, a group of doctors from around the world wrote to then health minister to voice concerns the helicopter service would not have a doctor on board when it was launched.
They were concerned that it could initially be staffed only with paramedics.
Northern Ireland's air ambulance service will be operational in 10-12 weeks, the Department of Health has announced.