Andal Ampatuan Jr is a local mayor and member of a powerful political clan in Maguindanao province on the southern island of Mindanao.
He has denied any responsibility for the killings.
Ampatuan Jr gave himself up to Jesus Dureza, a presidential adviser, in the provincial capital on Thursday and was expected to be flown to Manila for formal questioning, officials said.
"The family voluntarily surrendered him and they agreed that he will be investigated," Lt. Gen. Raymundo Ferrer, a military commander, said.
"The family voluntarily surrendered him and they agreed that he will be investigated," military commander Lt. Gen. Raymundo Ferrer said.
Ampatuan Jr has been named as the lead suspect in what is believed to be the Philippines' worst ever politically-linked killings.
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.