Troops take control
Lieutenant-Colonel Romeo Brawner, a military spokesman, said troops with a search warrant disarmed Ampatuan family members after entering the houses.
They were looking for weapons in the houses and a third house was being searched as well, he said.
Machine gun-mounted armoured vehicles stood guard outside the Ampatuan compound as thousands of government troops took control of the southern province.
More than 3,000 troops had earlier surrounded the Ampatuan compound and provincial government offices, as well as manning checkpoints leading to the compound, Brawner said.
He said that the forces were there to restrict movement within the compound and keep out supporters of the clan, which has ruled Maguindanao for a decade and has its own private army.
Friday's raids comes a day after soldiers unearthed a large cache of weapons, including mortars, machine guns, anti-tank bazookas, assault rifles and hundreds of boxes of ammunition from a vacant lot close to the Ampatuan compound.
Some of the boxes bore the initials of the Philippine Department of National Defence, prompting the military to launch an internal inquiry "to determine if these weapons and ammunition were issued by the government and if these were sold by some soldiers", Brawner said.
The illegal sales of military weapons and corruption in the army bureaucracy are issues raised in the past by soldiers who mounted coup attempts against Gloria Arroyo, the president.
Arroyo has come under intense pressure following the massacre because of her close political relationship with Ampatuan Sr, who helped delivered crucial votes for her campaign during the 2004 elections.
The president has promised swift justice in the killings, and her ruling party has since expelled the Ampatuans.
On Thursday Maguindanao's entire 1,092-strong police force was relieved of duty to ensure an impartial investigation of the killings, Ronaldo Puno, the interior secretary, has said.
Ampatuan Jr, named as the lead suspect by police, has been in custody since surrendering to the authorities three days after the massacre.
His father and six other family members have also been indicted in connection with the killings, and Agnes Devanadera, the justice secretary, said she would subpoena the governor and others for a preliminary investigation in Manila on December 14.
The Ampatuans deny any involvement.
Last week's massacre has triggered widespread condemnation inside and outside the Philippines.
|Ampatuan Sr, right, and his clan are known to be closely-linked to Arroyo, left [EPA]
The killings followed an ambush on a convoy of political campaigners and a group of accompanying journalists in a remote farming area of Maguindanao.
Police allege Ampatuan Jr and 100 of his gunmen shot dead the occupants of a convoy that included relatives of Esmael Mangudadatu, his rival for the post of provincial governor in elections scheduled for next year.
Mangudadatu has said the killings were carried out to stop him from running for office.
Fifty-seven bodies were later found off the highway, some on a grassy hillside and some buried in a pit.
Forensic findings indicated that some of the victims were mowed down with a light machine gun and others shot from a distance of just 60cm.
At least five of the female victims may have been raped, police said on Thursday.
About 30 of the slain victims were journalists.
On Thursday, protesters marched towards the presidential palace, demanding justice for the killed journalists and other victims, and local media groups are considering asking the United Nations to intervene in the murder investigations.