The Vatican has stressed Pope Francis’s commitment to press freedom before a meeting between the pontiff and the Maltese prime minister, Joseph Muscat.

The private meeting is due to go ahead despite calls in Malta for the pope to cancel it amid a political crisis triggered by the murder of the journalist Daphne Caruana Galizia.

A spokesperson for the Vatican said the content of private meetings was not usually disclosed, but added: “Recently [in May] during the meeting with the Italian Foreign Press Association, the Holy Father reiterated his absolute commitment to the freedom of the press, remembering the many journalists who have paid for it with their lives.”

Muscat, who announced on Sunday he would step down in January after weeks of protests, arrived in Rome on Friday to attend the Mediterranean Dialogues conference. Vanessa Frazier, Malta’s ambassador to Italy, confirmed the private meeting would go ahead as planned on Saturday morning.

It comes amid allegations that senior government figures attempted to interfere in the investigation into the October 2017 murder of Caruana Galizia, who was killed by a bomb planted beneath the driver’s seat of her rental car as she drove away from her home in the village of Bidnija. Caruana Galizia, 53, had exposed corruption at the highest level in Muscat’s government.

Timeline Recent developments in the Daphne Caruana Galizia murder investigation Show Malta’s prime minister, Joseph Muscat offers a presidential pardon to Melvin Theuma, a taxi driver from Birkirkara, in return for sharing potentially crucial evidence about the murder of the journalist Yorgen Fenech, a prominent Maltese businessman, is arrested onboard his yacht as it is heading out to sea. Fenech is released on bail and placed under round-the-clock police surveillance. The Maltese prime minister’s chief of staff, Keith Schembri, and the tourism minister, Konrad Mizzi, resign. The economy minister, Chris Cardona follows them. They have all denied any wrongdoing. Schembri is arrested. Details emerge that one of three men awaiting trial for the murder claimed they originally planned to shoot the journalist through a window where she often sat while working at home. Schembri is released. Muscat emerges from a marathon cabinet meeting at 3am on Friday to announce he will stay in the job until the murder investigation is complete. The European parliament agrees to send an 'urgent mission' to Malta over the case. Fenech is charged with complicity in Caruana Galizia’s murder. Muscat resigns. In a televised address he says he will stay on until a new leader of his ruling Labour party is elected in January.

Yorgen Fenech, a wealthy businessman who is accused of masterminding the murder, told a court on Thursday that he received regular tipoffs about the investigation from Keith Schembri, a former government chief of staff. Fenech was charged last week with complicity in the 2017 killing.

A group of 22 Maltese academics wrote a letter to Francis on Wednesday urging him not to meet the country’s leader.

“In our view it is totally unwise, and pastorally undesirable, to involve the Holy Father in a propaganda exercise in an attempt to postpone an inevitable outcome, given the serious and grave nature of the accusations and allegations which are plaguing the present administration of our country in full view of local and world media,” they wrote.

The Vatican never reveals details ahead of private meetings between the Pope and heads of state. However, the pontiff usually takes his cues from the bishops representing the country. In a statement on Thursday, the Maltese bishops Charles Scicluna, Mario Grech and Joseph Galea-Curmi called on citizens to “work together in these turbulent times, with a calm sense of purpose, to promote truth and justice with charity and respect for one another”.

On the second anniversary of Caruana Galizia’s death in October, Scicluna told a local news agency that he hoped those investigating her death “may bring to justice the perpetrators and anyone involved”.

Reports in the Maltese press said the Italian prime minister, Giuseppe Conte, had cancelled a meeting with Muscat in Rome, but Conte’s press office said it was unable to confirm whether the meeting scheduled for Friday would still take place.

At the start of a highly scrutinised inquiry into Caruana Galizia’s death on Friday, her family said she had lived in fear as she investigated government corruption.

“My mother feared for her safety,” Caruana Galizia’s eldest son, Matthew, told the independent inquiry. “She once told my brother that she felt they were frying her alive,” he added, in reference to a powerful lobby he alleged had launched an intimidation campaign against his mother over her stories. “The times our dogs were killed, when the front door of our house was set alight - those were threats.”

The family say the inquiry, headed by a retired judge, should focus on the crucial question of whether something could have been done to save Caruana Galizia’s life.