The declaration of martial law allows troops to make arrests without court warrants.
Gloria Macapagal Arroyo, the president, said she had ordered martial law in the province as "heavily armed groups [in the area] have established positions to resist government troops".
It is the first time in 28 years that such a drastic measure has been imposed anywhere in the country.
Within hours of martial law being declared, special forces stormed into the home of Andal Ampatuan Sr, the local governor, and took him into custody, the military said.
"He was taken at 2am [18:00 GMT on Friday] by Special Action Forces. He did not resist [arrest]," Major Randolph Cabangbang, the regional military spokesman, said.
Zaldy Ampatuan, one of the Ampatuan Sr's sons and the governor of an autonomous area in the southern Philippines, was also taken into custody on Saturday morning, according to the military.
Andal Ampatuan Jr, another son of the clan patriarch, is already languishing in a Manila detention centre after being charged with 25 counts of murder for the November 23 massacre that took place in a remote area of Maguindanao.
Police allege Ampatuan Jr and 100 of his gunmen shot dead the occupants of a convoy that included relatives of his rival for the post of Maguindanao governor in next year's elections, as well as a group of journalists.
Esmael Mangudadatu, Ampatuan's rival, said the killings were carried out to stop him from running for office.
Ampatuan Sr has ruled the strife-torn province since 2001 with the backing of his own private army, as well as the support of Arroyo's ruling coalition, and installed his family members into a myriad of government positions.
He had been grooming his son and namesake, a local mayor, to succeed him as governor.
Jesus Verzosa, the national police chief, said on Saturday that at least three other members of the Ampatuan clan were also wanted for their suspected links to the massacre.
Zainudin Malang, the director of the Bansamoro Centre for Law and Policy in the Philippines, described the introduction of martial law as "a political matter", for the national government to show that it was serious about dealing with the issue.
"This area has been under de facto martial law since the 70s. Even before they issued military law, we've had military checkpoints all over the place," he told Al Jazeera.