Joseph Church has been appointed Chief Electoral Commissioner despite no agreement having been reached with the Opposition.
An Opposition spokesman said it had discussed the appointment with the government but the two sides failed to reach an agreement.
Mr Church was proposed by the government. The Opposition, however, had suggested two other candidates for the post, who had held high positions within the civil service. It felt they were better suited to the position.
But the spokesman said that the government went ahead with its own candidate.
The Opposition had suggested two other candidates for the post
The Electoral Commission is set up in terms of the Constitution. Its members are appointed by the President acting in accordance with the advice of the Prime Minister, given after he has consulted the Leader of the Opposition.
Mr Church has occupied various positions within the public service, including director and director general at the Ministry of Health. For the past four years he has acted as secretary to the presidency.
He studied diplomacy at the University of Malta between 1996 and 1998 and Management and Human Resources between 2002 and 2004.
In a statement, the government thanked outgoing commissioner Saviour Gauci for his sterling service. Mr Gauci has since retired but will continue providing his services as a consultant.
The Commission, which is an autonomous body, revises the boundaries of electoral divisions and has the delicate task of conducting elections and referenda.
Its decisions have on occasion stirred controversy, such as when two years ago it denied the European Greens observer status during the divorce referendum, a position the Greens had been granted for the EU membership poll several years earlier.
Its next major job is to oversee the election of Maltese members of the European Parliament in a poll to take place on May 24.
It will be the third EP election held locally, with the Labour Party hoping to hold on to four seats of the six up for grabs and the Nationalist Party vying to increase their presence in the parliament to three seats.