Cutajar's resignation comes shortly after the resignation of Joseph Muscat as the island country's prime minister.
Malta's police chief resigned on Friday as part of a wave of government changes over criticism of the investigation into Daphne Caruana Galizia's murder.
The country's new prime minister Robert Abela has promised to improve the rule of law following multiple minister resignations over the journalist's assassination.
Police commissioner Lawrence Cutajar said he was resigning so that the new head of state could "implement the necessary reforms in the Police Force."
His resignation comes a week after Joseph Muscat left office over what many activists called a flawed investigation.
The 53-year-old investigative journalist was murdered by a car bomb outside her home in October 2017. The outgoing prime minister said he was "hurt" by the journalist's work when she was alive but that he "did not suffer as much as her family did" when she was murdered.
In December, the European Parliament passed a resolution detailing their concerns over the rule of law, independence of the police and judiciary, and credibility of the investigations into the murder.
Reporters without Borders had previously said that there was "no justice" for the journalist in a report detailing the flaws in the murder investigation. It wasn't until November - over two years after the journalist's death - that police arrested prominent businessman Yorgen Fenech over his alleged role.
Fenech's arrest led to the resignation of the country's tourism minister Konrad Mizzi and Muscat's chief of staff Keith Schembri.
"How they mocked us when, a day after my mother was assassinated, we called for the resignations of the prime minister, police commissioner, and attorney general and the investigation of Keith Schembri," tweeted Paul Caruana Galizia, the son of the investigative journalist.
"Watch them fall," he said.