Angelo Gafa was appointed as police commissioner on Tuesday, following the go-ahead on Monday of parliament's public appointments committee.
The committee's meeting was boycotted by the Opposition, which disagreed with the manner of appointment.
Gafa was selected after a call for applications which drew 14 applicants. The applicants were interviewed by the Public Service Commission and a shortlist of two passed to the government, which opted for Gafa.
The method of appointment, a break from the direct appointment of the past, had been welcomed by the Council of Europe's Venice Commission, but the opposition had argued that the commissioner should be appointed with the support of two-thirds of the members of the House of Representative to ensure there was no political inference.
The opposition also objected to the one year probationary period for the commissioner.
Labour MEP and former prime minister Alfred Sant in a tweet on Tuesday also came out against the probationary period, saying it does not make sense.
Gafa is a former investigator and police inspector who served for the past few years as the corp's first CEO.
He succeeds Lawrence Cutajar, who stepped down in January after enduring criticism if failing to investigate several allegations involving the government, claims which he denied.