"They are not true. My conscience is clear," he said before being flown out of the province aboard an army helicopter.
"The reason I came out is to prove that I am not hiding and that I am not guilty."
His surrender came 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.
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 said.
|The first funerals of victims of the massacre were held on Thursday [EPA]
The killings took place after a convoy carrying aides and relatives of a rival politician, Esmael Mangudadatu, as well as a group of accompanying journalists, was ambushed by suspected Ampatuan gunmen.
The convoy was on its way to file election papers nominating Mangudadatu as a candidate for provincial governor in elections next year.
Ampatuan Jr's father is the current provincial governor who had reportedly been grooming his son to succeed him, setting the stage for a show-down with the rival Mangudadatu clan.
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.
At least 10 of those killed were motorists who were passing by on the highway and had apparently witnessed the abduction.
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.
On Friday in a getsure of defiance he filed his candidacy papers in person in the Maguindanao provincial capital, vowing to continue his campaign for the governorship.
"Only death can stop me from running," Mangudadatu told reporters, escorted
by soldiers, a police commander and a senior army general.
"This symbolises our freedom," he said, holding up his certificate of candidacy in front of followers.
"I hope this will be the start of our liberation."
Earlier this week Mangudadatu said four witnesses in his protection had told him that the ambush was a premeditated attack, with the killing ground and graves prepared well before the massacre took place.
"It was really planned because they had already dug a huge hole [for the bodies]," he told reporters.
Among those killed was Mangudadatu's wife and several close family relatives.
Also killed were at least 22 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.