Twenty-two bodies had previously been found in a remote farming area of Maguindanao following Monday's Nov 23, killings by gunmen allegedly linked to the area's political kingpin.
The group abducted associates of a rival politician and a large group of journalists who were covering them.
"All 13 bodies were pulled from one grave," National Police chief Jesus Verzosa told new agency by phone from the scene of the massacre in Maguindanao province.
Verzosa said he feared the death toll could rise with several other members of the kidnapped party of more than 40 people still missing.
Journalists on the scene said a mechanical digger was emblazoned with the name of the Maguindanao provincial governor, Andal Ampatuan, whose bodyguards had been blamed by the military as being behind the massacre.