A spokesman for the Yobe State government said on Tuesday that 47 "rebels" had been detained since Friday and that five had been killed, along with three women and two children caught up in a raid on their border hideout.
Seven of those arrested were picked up by police officers from neighbouring Niger, acting as guards on its porous frontier with the Nigeria's remote and arid northern savannah, junior spokesman Alkali Jajere said.
The Muhajirun group, which openly claims inspiration from Afghanistan's hardline Taliban movement, was thought to count around 200 members, mainly middle-class graduates from the northeastern city of Maiduguri.
The group has launched a series of attacks in the past three weeks on police stations in the northern state of Yobe and along Nigeria's northern border with Niger, killing at least two officers.
Many of the radicals are thought to have melted away into the population, but their leader - nicknamed "Mullah Omar" after the Afghan Taliban's fugitive figurehead - has been arrested, Jajere said.
"Security forces are still looking for other members of the group, who have disappeared or melted into the community. We know this will be difficult," Jajere said.
Army spokesman Chukwuemeka Onwuamaegbu said Yobe's governor, Bukar Abba Ibrahim, had appealed to President Olusegun Obasanjo to send in troops "to assist the police to curb the violent activities of the bandits."
The men were detained on the
border with Niger
"Soldiers were sent in last week and they have been able to dislodge the bandits. The place is now peaceful," he added.
"I know they have been flushed out of Yobe State. I don't know where they have run to. Our soldiers are still on the ground to ensure that they don't operate from there anymore," he said.
Nigeria is Africa's most populous country and slightly more than half of its 126 million citizens are Muslims, most of them living in 12 northern states in a region once ruled by emirs and populated by nomads.
The vast majority of Nigeria's Muslims now live peacefully under the country's secular federal constitution, and Christian president, but ethnic and sectarian tensions are never far from the surface.
Nigeria is Africa's most populous
Riots between Muslims and Christians have killed thousands of Nigerians since the end of military rule in 1999, while the reintroduction of Islamic Sharia law has stoked tensions in northern cities.
But so far there has been no evidence of "armed Islamist militias or terror cells", despite a call last year from Saudi-born Usama bin Ladin for Nigerian Muslims to topple their "apostate" regime.
The Muhajirun moved into Yobe from neighbouring Borno State last year and attempted to set up a community run on strict Islamic lines in the remote border area around Kanama, just south of Niger's Mandaram region.
Police were called in after disagreements between the radicals and local villagers. Last month clashes erupted that saw at least three police stations burned down and one officer killed.
On Friday last week the group stormed into Yobe's capital Damaturu, killing a second policemen and triggering the weekend's severe clampdown, in which army soldiers were deployed against it.