Ampatuan Jr has been named as the lead suspect in what is believed to be the Philippines' worst ever politically-linked killings.
His father, Andal Ampatuan Sr, is the provincial governor who has been grooming his son to succeed him in elections due next year.
The family also has close political ties to the Philippine president, Gloria Arroyo, although on Thursday officials in Arroyo's party said Ampatuan Jr, his father and a brother had been expelled following an emergency meeting of the party leadership.
Following his surrender, Ampatuan Jr was taken into military custody and flown out of the provincial capital in an army helicopter.
Asked by reporters if he was involved in the killings, Ampatuan Jr, who tried to hide his face with a scarf, replied: "There is no truth to that. The reason I came out is to prove that I am not hiding and that I am not guilty."
Ronaldo Puno, the Philippines interior secretary, said he had warned the family they risked a military attack unless Ampatuan Jr gave himself up by midday on Thursday.
His surrender comes as a man who says he was a witness to Monday's killings told Al Jazeera that Ampatuan Jr had directly ordered the massacre, targeting a political rival for the provincial governorship.
"Datu Andal himself said … anyone from the Mangudadatu clan - women or children - should be killed"
Witness to massacre
The witness, who identified himself only as "Boy", said he was among more than 100 armed men who held up a convoy of political campaigners and journalists before taking them to a remote mountainous area.
He said Ampatuan Jr had ordered the gunmen to kill all the members of a rival political clan, including women and children, and to make sure no evidence was left behind.
"Datu Andal himself said… anyone from the Mangudadatu clan - women or children - should be killed," he told Al Jazeera.
"We don't ask why, we just follow orders."
"Boy", who is now in hiding fearing his life is in danger, said all of the women in the group had been raped before being killed and their bodies dumped in mass graves that had already been dug out using an excavator.
On Thursday, security forces said they had arrested 20 other people in connection with Monday's massacre.
|The dead include at least 20 journalists who were travelling with the convoy [Reuters]
The arrests come after police at the scene of the massacre discovered another 11 bodies buried in shallow graves, taking the death toll to at least 57.
The first funerals of some of the victims also took place on Thursday, more than three days after the massacre, although the bodies of several others have yet to be identified.
The killings occurred after about 100 suspected Ampatuan gunmen allegedly ambushed a convoy of aides and relatives of a rival politician, Esmael Mangudadatu, as well as a group of accompanying journalists.
The victims were snatched as they were travelling to file election papers nominating Mangudadatu as a candidate for provincial governor in next year's poll.
According to investigators, the victims were shot at close range, some with their hands tied behind their backs, before being dumped or buried in shallow graves on a remote hillside.
Mangudadatu, the rival candidate for governor, was not himself in the convoy because he had received death threats and said he thought the women he sent in his place would be safe.
He has pressed senior Philippine government officials to immediately arrest and prosecute those behind the killings.
Mangudadatu said four witnesses in his protection had told him the convoy was stopped by armed men loyal to Ampatuan Jr, to prevent his family from filing election papers.
"It was really planned because they had already dug a huge hole [for the bodies]," he told reporters earlier this week, adding that there were reports from the area that the militia had been blocking the road for a few days.
Among those killed were at least 20 journalists accompanying the convoy, in what media monitoring groups have labelled as the worst-ever single attack on journalists anywhere in the world.
The massacre has put intense pressure on the government of Gloria Arroyo, the Philippine president, to take decisive action against the Ampatuan clan.
She has vowed an all-out effort to bring those responsible for the killings to justice, saying that no one would be seen to be above the law.
In the wake of the massacre Arroyo declared a state of emergency in Maguindanao and a neighbouring province, ordering hundreds of extra troops to the area.