The Maltese prime minister’s chief of staff, who resigned this week, has been arrested and questioned by police over allegations that he is a co-conspirator in the murder of the investigative journalist Daphne Caruana Galizia. Keith Schembri, a businessman who has run the office of the prime minister, Joseph Muscat, since the Malta Labour party came to power in 2013, was arrested on Tuesday, police sources confirmed.

It is understood he was taken into custody after allegations by the businessman Yorgen Fenech, who was arrested last week after trying to leave Malta on his yacht.

Fenech, who is himself under suspicion for involvement in the killing, is understood to have implicated Schembri in the hope of receiving a presidential pardon. Caruana Galizia, Malta’s foremost investigative journalist, was killed in October 2017 when a bomb fixed to her car was detonated near her home in the village of Bidnija. She had exposed corruption at the highest levels in government and business circles.

The killing of a prominent journalist in a European Union member state drew international attention and raised concerns about the rule of law in Malta.

Caruana Galizia’s family said they were seeking an urgent meeting with the attorney general, Peter Grech, in an effort to prevent Fenech from being granted a pardon. “We urgently want to clarify the situation,” the family said.

An official in the attorney general’s office said he would meet the family to discuss their concerns.

Lawyers for Schembri and Fenech did not respond to requests for comment. Maltese police have made no statement.

In a further development, a doctor has been arrested, accused of passing messages between Schembri and Fenech. According to local reports, citing police sources, Dr Adrian Vella is suspected of passing messages to Fenech while the businessman was on police bail and in hospital under supervision by officers. At that point, Schembri had not yet resigned. The doctor was close to Schembri, reports said, having accompanied him on trips for medical treatment in recent years.

Vella’s lawyer did not respond to a request for comment.

The revelation will add to the pressure on the prime minister to step down. Muscat yesterday lost a key ally when the influential newspaper Malta Today withdrew its support. The paper’s co-owner was known to be close to Muscat.

“Joseph Muscat’s moral authority has been compromised to the point of no return,” the paper’s executive editor wrote in a scathing editorial. “The stage is set for Muscat’s exit.”

The prime minister is reportedly planning to address a Labour party rally on Sunday. But, in a Facebook post yesterday, his education minister, Evarist Bartolo, undermined the show of support, warning against raising the political temperature and saying it was not the time for “hot heads and spreading hatred and violence”.

He added: “Protests are essential in a democracy, but they have to be civil and democratic because it is easy to spark the crowd, but then how to put out the fire?” The opposition Nationalist party has cancelled an event on Sunday after criticism that it could also inflame the situation.

Caruana Galizia’s family have urged supporters to attend demonstrations organised by campaign groups and avoid party political events. “DO NOT go to any rallies organised by party leaders,” her son Matthew Caruana Galizia wrote on Facebook. “This is not a time for tribal politics. Joseph Muscat wants us to go to war against each other. Our war is against corruption.”

Schembri was arrested after tendering his resignation on Monday night, following a long meeting at Muscat’s home. For nearly four years, he has been at the centre of a political scandal triggered by Caruana Galizia’s investigations.

Using a leak of offshore information known as the Panama Papers, she reported that Schembri and a fellow minister, Konrad Mizzi, had become the beneficiaries of secretive offshore companies soon after entering office. Subsequent investigations uncovered that those companies were due to receive payments from another shell company, belonging to Fenech.

The businessman was granted a valuable concession by the government to run a power station, while Mizzi was energy minister. Mizzi resigned on Tuesday, saying he was guilty of poor judgment but innocent of any criminal conduct.

Schembri has previously denied all allegations of wrongdoing.

A suspected middleman, Melvin Theuma, was granted a presidential pardon in exchange for information on Monday, and is scheduled to testify before a magistrate tomorrow.

Three accused hitmen - Alfred Degiorgio, his brother George, and Vincent Muscat - are also in detention following their arrest in December 2017, but have not yet been brought to trial. They have been charged with planting the explosive device that killed Caruana Galizia.

The campaign group Reporters Without Borders called for all those implicated in the murder to be brought to trial.

“After two long years of impunity, we welcome the significant developments that now appear to be taking place in the investigation into the assassination of Daphne Caruana Galizia. However, these are not sufficient steps towards justice. We call for all hitmen, all middlemen, and all masterminds to be prosecuted to the full extent of the law,” its UK bureau director, Rebecca Vincent, said.

Yesterday there were clashes in Malta’s parliament, with opposition MPs staging a walkout from the House of Representatives in protest at what they said was the prime minister’s refusal to shoulder political responsibility.

Before leaving the chamber, the Nationalist party leader, Adrian Delia, called on Muscat to resign and announced the Nationalists would no longer speak to a “government that has lots its legitimacy, since the prime minister does not recognise his political responsibility”.