Security forces hunted door-to-door for Islamic militants in northern Nigeria on Thursday after killing more than 100 of them by storming the sect's compound. A top rights group said innocent people were getting executed in the process.

The government, which blames the Boko Haram sect for instigating days of violence in the mostly Muslim region, shelled and stormed the group's mosque and headquarters Wednesday night, setting off a raging firefight with retreating militants.

Sect leader Mohammed Yusuf escaped along with about 300 followers but his deputy was killed, according to Army commander Maj. Gen. Saleh Maina.

The bodies of barefoot young men littered the streets of Maiduguri on Thursday morning as the army pursued the manhunt on the outskirts of the city. Police said most of the dead were Islamist fighters.

A local rights group charged Thursday that security forces have been killing innocent civilians as they fought to crush the sect. Witnesses said they watched troops executing people alleged to be militants.

An AP reporter saw soldiers, under fire, shoot their way into the sect's mosque in Maiduguri on Wednesday and then rake those holed up inside with gunfire. The reporter later counted about 50 bodies inside the building and another 50 in the courtyard outside.

Another five corpses were just inside a large house near the mosque. Maina pointed to the body of a plump, bearded man and said it the Boko Haram sect's vice chairman, Bukar Shekau.

"The mission has been accomplished," said Maina, the army commander.

The militants, armed with homemade hunting rifles and firebombs, bows and arrows, machetes and scimitars, were no match for the government forces.

Army Col. Ben Anahotu said three police officers were also killed in the battle.

Militants seeking to impose Islamic Shariah law throughout this multi-religious country attacked police stations, churches, prisons and government buildings in a wave of violence that began Sunday in Borno state and quickly spread to three other northern states.

It is not known how many scores of people have been killed, wounded and arrested. As of Wednesday, officials said at least 4,000 people have been forced from their homes.

The epicenter of the violence has been the Boko Haram headquarters in Maiduguri, capital of Borno state. Maina said his troops would fire mortar shells later Thursday to destroy what is left of the sprawling compound, which stretches over 2.5 miles (4 kilometers).

Maiduguri resident Linda Dukwa said she and her family have been hiding in terror for days, too scared to venture out even for food, after police executed two men in front of her Monday.

"They were dressed in white robes," she said, indicating they were sect members. "They were held by policemen. Then they shot their feet. After they fell on the ground, they (police) shot their heads."

"It was terrifying," she said.

League for Human Rights director Shamaki Gad Peter said rights workers saw the bodies of up to 20 people after Wednesday's government offensive against the sect compound began. The bodies were unarmed and some appeared to have been shot from behind, possibly trying to escape the mayhem, he said.

Police had warned people to evacuate the area.

Nigeria's security forces are notoriously trigger-happy but have a difficult job trying to target sect members who are reportedly using innocents as human shields in the congested urban area.

"We respect the rules of combat," national police spokesman Emmanuel Ojukwu said when asked about the allegations of executions. He added that troops were "gradually restoring order."

The radical sect is known by several different names, including Al-Sunna wal Jamma, or "Followers of Mohammed's Teachings" and "Boko Haram," which means "Western education is sin."

Some Nigerian officials have referred to the militants as Taliban, and analyst Nnamdi K. Obasi of the International Crisis Group said a few have actually fought with that radical movement in Afghanistan.

Obasi said sect leaders have also traveled to meet and train with other radically minded groups in Sudan, Iraq and particularly Iran, which they consider "a destination of pilgrimage."

Nigeria's 140 million people are roughly divided between Christians in the south and northern-based Muslims. Shariah was implemented in 12 northern states after Nigeria returned to civilian rule in 1999 following years of oppressive military regimes. More than 10,000 Nigerians have died in sectarian violence since then.

Dire poverty is at the heart of the violence, with Boko Haram members angry that full Shariah has not been implemented, especially the law's demand for a social welfare system helping poor people.

In recent months, police have been raiding militant hideouts and finding explosives and arms. The house at the compound in Maiduguri included a laboratory the military said was used to make bombs.

President Umaru Yar'Adua said earlier this week the sect was preparing to unleash "the holy war." Security agents were ordered to attack when the movement began gathering fighters from nearby states at its Maiduguri headquarters, he said.

Borno Gov. Ali Modu Sheriff told journalists that sect leader Yusuf was seen Wednesday night in a village 28 miles (45 kilometers) northeast of Maiduguri.

Men in Bauchi state and in Maiduguri, meanwhile, started trimming and even shaving off their beards, fearful that security forces could mistake them for religious fanatics.

In violence elsewhere, Nigeria's Vanguard newspaper reported that militants attacked security forces in Yobe state on Wednesday, and quoted police as saying that 43 sect members were killed in a shootout near the city of Potiskum.

Police in Bauchi state have reported 42 people killed, including two soldiers and a police officer, 67 hospitalized with serious injuries and 157 men arrested.

In the city of Kano, the local government bulldozed a mosque and the house of a sect leader on Wednesday, saying it was an illegal structure, just days after sect militants attacked a Kano police station. Kano police spokesman Baba Mohammed said more than 50 militants have been arrested, with five shot and killed during the arrests.

Boko Haram is reported to include many members of the elite, including university lecturers and others who have abandoned their jobs and sold their homes to join. Vanguard and the Nigerian Guardian newspaper reported that police in northwest Sokoto state on Tuesday arrested former university lecturer Kadiru Atiku, believed to the sect's local leader.

Analysts say the latest violence reflects decades-old grievances of Nigerians whose governments are so corrupt and ineffective they do not deliver even basic services like running water and electricity.