An AFP photographer witnessed armoured personnel carriers patrolling highways in the southern province of Maguindanao and television footage showed police commandos surrounded buildings in major towns controlled by the clan.
National police chief Director General Jesus Verzosa said security forces had arrested some of the gunmen linked to Monday's massacre while the army said it was hunting for many other suspects.
"Most of the armed group that perpetrated this crime have run away towards the mountainous area of Maguindanao," military spokesman Lieutenant Colonel Romeo Brawner said on ABS-CBN television.
"That is where we are conducting our pursuit operations."
He said the army has also disbanded the provincial Civilian Armed Forces Geographical Unit, militiamen under the control of the family of the alleged massacre mastermind, Andal Ampatuan Jnr.
National police spokesman Chief Superintendent Leonardo Espina said the entire police force which had been providing security at Ampatuan Jnr's office had been relieved.
Ampatuan Jnr is the mayor of a town in Maguindanao while his father of the same name is the provincial governor.
Police said about 100 Ampatuan gunmen allegedly abducted a convoy of aides and relatives of a rival politician, Esmael Mangudadatu, plus a group of journalists, on Monday.
The victims were snatched as they were travelling in a six-vehicle convoy to nominate Mangudadatu as the opposition candidate for provincial governor in next year's elections.
They were shot at close range, some with their hands tied behind their backs, and dumped or buried in shallow graves on a remote farming road close to a town bearing the Ampatuan name.
Fifty-seven bodies have been recovered so far, and police are still searching for more possible victims.