Alijol Ampatuan is the sixth person among witnesses, potential witnesses or their relatives killed since the case went to court in 2010, said prosecutor Nena Santos.
The man was a victim of a drive-by shooting in February, she said.
He was related to the powerful Ampatuan clan, accused of the 2009 killings.
Prosecutors had wanted to approach the man, who was alleged to have sent gunmen to take part in the massacre, to testify at the trial as a state witness.
The dead included many female members of a rival political family, the Mangudadatus, as well as 30 reporters travelling with them.
The massacre took place as the Mangudadatu group travelled to file candidacy papers for a provincial election.
Human Rights Watch says that whoever is behind the killings is sending a clear message of intimidation.
The rights group has warned that other witnesses will not come forward if the Philippine government does not offer better protection, reports the BBC's Kate McGeown in Manila.