Foreign Minister Stephen Smith and Defence Minister John Faulkner said the first element of the 180-member medical task force would depart Australia aboard a RAAF C-17 transport aircraft from from RAAF Base Amberley, in Queensland today.
The rest will deploy in coming weeks.
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The ministers said the joint operation between AusAID and the Australian Defence Force would contribute to Pakistan's government and international efforts to address growing health concerns including outbreaks of water-borne diseases.
The Australian team, called the Joint Inter-Agency Medical Task Force, will establish a facility near Kot Addu, in the vicinity of Multan, in the Muzaffar Garh District of the Punjab Province.
There are some 800,000 people in the region, with an estimated 27,000 displaced by the floods.
The task force will comprise defence and civilians, including doctors, nurses, paramedics and support personnel from state health agencies.
It includes three defence primary health teams, an environmental health team and an AusAID rapid response team.
They will provide a wide range of services including midwifery, dental pathological, pharmaceutical, radiological and environmental health capabilities.
This is all being coordinated by the Australian government through Emergency Management Australia.
Mr Smith said Pakistan was a good friend and Australia was currently focused on the immediate needs of the Pakistani people.
"But we will also assist with the recovery and reconstruction task," he said in a statement.
"We stand ready to provide whatever assistance we can.
"The medical teams will provide essential and immediate primary health care to treat people in central Pakistan and help prevent the spread of disease."
A defence spokeswoman said engineers would be part of the group to support the delivery of clean water and construction of accommodation and other buildings for the task force.
After that was completed they would help deliver support to the local people.
"The Pakistan Military will provide security for the health teams," she said.
"The security threats in Pakistan have been reviewed and the Australian commitment will deliver its emergency relief within certain force protection measures."
Earlier this month, two C-17 flights flew to Islamabad to deliver tents and tarpaulins for about 12,000 affected families, water storage and purification equipment, 24 portable generators, birthing kits for almost 2000 expectant mothers plus other medical supplies.
Senator Faulkner said the task force could remain for an extended period but would maintain close links with the Pakistan government to ensure it was providing support only as long as needed.
"Our people will be operating under challenging conditions. The task force will apply a range of preventive and force protection measures so they can complete their mission safely," he said.
As the government remains in caretaker mode, Senator Faulkner said he had sought and received the agreement of opposition defence spokesman David Johnston on the ADF commitment to Pakistan.
