Lawyer Romel Bagares said his client Efren Morillo and other petitioners also asked the court to order police to stop threatening witnesses.
More than 7,000 drug suspects have been killed since President Rodrigo Duterte took office in June and ordered the crackdown, alarming human rights group and Western governments.
Four policemen shot Morillo and four other men in impoverished Payatas village in metropolitan Manila in August.
Morillo, a 28-year-old vegetable vendor and the four slain men, were garbage collectors who were shot with their hands bound and could not have possibly threatened police, the petition said.
Three of the victims were ordered to kneel on the ground at the back of the shanty before they were shot to death. The last to be killed "begged to be spared, hugging the legs of one of the armed men and sobbing. As he would not let go of his hold, the man shot him on the nape," the petition said.
According to Bagares, police kill drug suspects then make it appear the victims died while fighting back.
"Because he survived the attack of the perpetrators and identified each and every one of them, his life is in grave danger," Bagares said in his petition, which asked the court to prohibit the police officers from entering an area 5 kilometers from the homes and workplaces of Morillo and other petitioners, who include the other men's relatives.
While acknowledging that some rogue police may have illegally killed innocent people, Dela Rosa stressed that 33 officers had been killed and more than 100 others wounded in clashes with drug suspects.
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