Villarante, of DZJV Radio and the local newspaper Laguna Score, was shot and killed by a gunman outside his house in Santa Cruz City in central Laguna Province. After being shot once, Villarante ran inside his home. While his relatives helped him outside again to get to a hospital, the gunman shot Villarante twice in the head, killing him instantly.
Villarante was known for his critical reports on allegedly corrupt local officials and drug traffickers. An editor of Laguna Score told journalists he believes that Villarante was murdered in reprisal for his work, and that the reporter had received numerous death threats in the past.
On August 26, police in Laguna announced that they had arrested Senando Palumbarit, identified in press reports as a civilian police agent, as a suspect in Villarante's murder. The National Bureau of Investigation said that Palumbarit's arrest was based on a police sketch of the suspect. Palumbarit denied involvement in the murder.
Local journalists have expressed concerns that the investigation into Villarante's killing has not been conducted in a thorough and impartial manner, and that Palumbarit's arrest is part of a police effort to protect high-profile individuals who may be responsible for killing the journalist. Soon after the murder, Santa Cruz Police Chief Superintendent Renato Paras told The Philippine Daily Inquirer that investigators were hesitant to reveal too many details about the case because high-profile individuals could be behind the killing.
Soon after Villarante's murder, police ransacked his house and confiscated a number of articles he had written, according to the Philippine Star newspaper. Villarante's sister told the Star that during the search, officers treated her family and her deceased brother as criminal suspects. The regional police superintendent has ordered an investigation into the incident.
After trial proceedings began in 2006, a judge dismissed the case against Palumbarit because witnesses were unwilling to testify, according to news reports.