The Reporters Without Borders (RSF) said witness Gury Ladica was shot and killed in Zamboanga del Sur last week after implicating a senior police officer in the murder of journalist Edgar Damalerio.
Damalerio, 33, a broadcaster and editor of a community newspaper, was shot and killed in May after exposing alleged corruption in the police force. He was the fourth journalist to be killed in the past 17 months in the strife-torn south.
"The murder of a person benefiting from a witness protection program established by the government is a very serious violation of the rule of law and shows how determined the killers of journalist Damalerio are to eliminate the witnesses," RSF Robert Menard said in a letter to Interior and Local Government Secretary Jose Lina.
But provincial police chief Pedrito Reyes denied the RSF accusation, saying there were no reports that a man named Gury Ladica was killed in the province.
He said a pro-government militiaman, Jovy Lovitania, was ambushed by unidentified gunmen while on his way home near Pagadian City, but that it appeared to have no connection with the reporters case.
"I am sorry to say that what the RSF has claimed is not true. There were no reports of any killing, except the ambush of this militiaman and his killing has nothing to do with any case," Reyes said.
Another witness in the case, Edgar Amoro, is under police protection, Reyes said.
The RSF, however, said two other witnesses, who were with Damalerio at the time of his death, have told the group they feared for their lives.