Larry Que, publisher of the Catanduanes News Now newspaper, is the first journalist killed since President Rodrigo Duterte assumed office in June; two others have been attacked and injured.
The Philippines is one of the world's most dangerous countries for media workers, according to a watchdog group.
Que was shot by an unidentified person on the remote central island of Catanduanes on Monday, Joel Sy Egco, the executive director of the presidential task force on media security, told CNN.
He died early Tuesday, according to a statement by the International Federation of Journalists (IFJ).
"Que's murder came after he published his column, which criticised local officials and their alleged negligence in allowing the setting up on the island-province of a recently raided shabu [the local name for methamphetamine] laboratory that authorities claimed was the biggest so far discovered in the country," the IFJ said.
According to the National Union of Journalists of the Philippines (NUJP), a second journalist, broadcaster Jinky Tabor, who was a witness to the raids that discovered the lab, has received death threats.
Que had only been publisher of the newspaper for two weeks, according to the NUJP, which said he was shot in the head as he was about to enter the building that houses his insurance office. The column in question was published in the December 13-19 edition of the newspaper.
The New York-based Committee to Protect Journalists (CPJ) has called on authorities in the Philippines to establish the motive behind Que's killing and bring the perpetrators to justice.
"President Rodrigo Duterte has sent mixed messages on his government's commitment to protecting journalists and upholding press freedom. He should set the record straight by quickly solving Que's killing through legal means," Shawn Crispin, CPJ's senior Southeast Asia representative, said in a statement.
A total of 77 journalists have been killed in the Philippines since 1992, according to the CPJ, which ranks it fourth in its Global Impunity Index, which spotlights countries where journalists die and their alleged killers go unpunished. It ranks behind Somalia, Iraq, and Syria.
Duterte has launched a brutal war on drug crime that has left more than 5,900
people dead since July.
Before he took his oath of office, Duterte said journalists killed on the job
in the Philippines were often corrupt.
"Just because you're a journalist you are not exempted from assassination, if you're a son of a bitch," he said. "Freedom of expression cannot help you if you have done something wrong."
But, in October, he created a task force
to protect the media from threats and violence and look into unsolved attacks.