Abdalla Hamdok's announcement came two days after gunmen in the region killed at least 20 civilians, including children, as they returned to their fields for the first time in years, the latest in a string of violent incidents.
The impoverished western region has seen years of conflict since an ethnic minority uprising prompted the government to launch a scorched-earth campaign that left 300,000 people dead and displaced 2.5 million.
"A joint security force will be deployed in the five states of the Darfur region to protect citizens during the farming season," Hamdok's office said in a statement after he met a delegation of women from the region.
The force will include army and police forces, it said.
Violence in Darfur has eased since Bashir's ouster by the army amid mass protests against his rule last year, with a preliminary peace deal signed in January between the government and a coalition of nine rebel groups, including factions from the region.
Farmers displaced in the conflict have since started to return to their land under a government-sponsored deal reached two months ago, in time for the July-November planting season.
But bloodshed has continued, particularly over land rights, according to expert Adam Mohammad.
"The question of land is one cause of the conflict," he said.
"During the war, peasants fled their lands and villages to camps, and nomads replaced them and settled there."
On Friday, armed men drove into a village and killed 20 civilians returning to their fields for the first time in years, an eyewitness and a tribal chief told AFP.
In late June and early July, hundreds of protesters camped for days outside a government building in the Central Darfur town of Nertiti to demand that the government beef up security after multiple killings and looting incidents on farmland and properties.
Bashir is wanted by the International Criminal Court over charges of genocide and crimes against humanity in the conflict.