Troops have found several weapons caches in the Shariff Aguak area
Philippine armed forces and police say they are pursuing at least 3,000 armed men loyal to the Ampatuan clan in the southern province of Maguindanao.
Manila has accused the clan of ordering the massacre of 57 people last week and of fomenting rebellion.
Officials said gunmen fired on troops in the first violence since martial law was declared in the province.
Rights groups have said they would challenge the imposition of martial law in the Supreme Court.
Troops have cordoned off the province, confiscated weapons caches and arrested scores of alleged gunmen.
Police commandos came under fire on Sunday as they patrolled near Datu Unsay, the town controlled by the chief suspect in the 23 November massacre, Andal Ampatuan Jr.
"Suddenly they [the police] were fired upon and there was an exchange of gunfire. They were not able to move so they called in reinforcements," said the chief of the Philippines National Police, Jesus Verzosa.
He said there were no casualties among the police.
On Monday, the government said it had taken full control of Shariff Aguak, the capital of Maguindanao province, and Defence Secretary Norberto Gonzales reportedly led government employees in a symbolic flag raising and singing of the national anthem.
The staff pledged allegiance to the government as armoured personnel carriers patrolled highways and heavily armed troops guarded government buildings.
But military officials told reporters that many local residents still feared the Ampatuan clan.
Prosecutors have drawn up charges of rebellion in addition to those of murder lodged against members of the Ampatuan clan - which has denied involvement in the massacre.
The clan has long controlled Maguindanao and its members have been loyal supporters of President Gloria Arroyo.
The murders were allegedly carried out to prevent a rival of Andal Ampatuan Jr from running for governor of the province in next year's elections.
Mr Ampatuan Jr has been charged with 25 counts of murder. His father, former Maguindanao governor Andal Ampatuan Sr, and three of his brothers were among suspects held last week.
President Gloria Arroyo's critics and human rights groups have criticised the declaration of rebellion because it gives a political gloss to the crimes and allows suspects to be granted bail and presidential amnesty.
These same groups are preparing a challenge in the Supreme Court to the declaration of martial law.
The security forces say martial law is allowing them the freedom they need to move against the Ampatuan empire.
But many Filipinos are uneasy about the methods being used to do what should have been done long ago, says the BBC's South East Asia correspondent Rachel Harvey.
Some Arroyo critics say she may move to extend martial law across the country in a bid to hold on to power after her term ends next year.