VALLETTA, Malta — More than two years after a car bomb killed Malta’s best-known investigative journalist, prosecutors in the Mediterranean island nation on Saturday charged a wealthy Maltese businessman with complicity in her murder and other crimes.

The arraignment of the businessman, Yorgen Fenech, a member of one of Malta’s most prominent and richest families, capped a tumultuous week in which a long-stalled investigation into the murder of the journalist, Daphne Caruana Galizia, suddenly picked up pace, ensnaring senior members of the government and Malta’s business elite.

Mr. Fenech, 38, who is suspected of paying three contract killers to carry out the murder, pleaded not guilty. He was arrested on Nov. 19 while trying to flee Malta aboard his yacht. Maltese military personnel halted the vessel as it set out to sea from a marina built by Mr. Fenech’s family conglomerate, Tumus Group, and forced it to return to port.

The killing in October 2017 caused outrage across Europe, putting a harsh spotlight on Malta, the smallest member of the European Union and a country denounced as a “mafia state” by Matthew Caruana Galizia, the journalist’s oldest son.

Speaking after Mr. Fenech’s arraignment on Saturday evening, Mr. Caruana Galizia said it was “surreal and horrifying” to sit in court just a few feet from a man suspected of ordering and paying for the murder of his mother, who was 53 when she died.

In a statement read outside the courthouse in Malta’s capital, Valletta, family members demanded the immediate resignation of Prime Minister Joseph Muscat, saying that only his departure would allow a “free and full investigation.”

Maltese news media outlets reported on Friday that Mr. Muscat planned to announce his resignation “imminently,” but by late Saturday night he had not done so despite widespread suspicions that some of his close associates in government may have been involved in the murder plot.

Earlier on Saturday, protesters gathered in the capital for the latest in a series of small but noisy demonstrations demanding that the prime minister step down. They chanted, “Out, out, out!” and waved signs reading “Enough corruption” and “Blood is on your hands.”

No evidence has come to light linking the prime minister to the plot against Ms. Caruana Galizia, who was a fierce critic of Mr. Muscat and his associates in the governing Labour Party. But police investigators have in recent days questioned his chief of staff, Keith Schembri, and other associates regarding the case. Earlier this week, Mr. Fenech had offered to supply information linking them to the murder if he was pardoned.

Mr. Schembri resigned on Tuesday, along with two ministers who are also suspected of possible involvement in, or knowledge, of the plot. None have been charged.

At a hearing attended by Ms. Caruana Galizia’s parents, her three sons and her three sisters, Mr. Fenech stood impassively in a charcoal gray business suit as the charges were read: complicity in murder, membership of a criminal organization and a charge related to an illegal explosion. They carry a maximum sentence of life imprisonment.

As recently as a few weeks ago, it appeared that the murder inquiry would never proceed beyond three professional criminals who were arrested in December 2017. They were accused of planting a bomb in the journalist’s car and then detonating it by cellphone as she drove away from her family’s home on a country road.

The three men had no obvious reason to want Ms. Caruana Galizia dead, and answers to why she had been killed and who ordered the attack remained stubbornly elusive.

All of that began to change recently when the police stumbled on a suspected middleman in the plot who was arrested in November in connection with a separate case. Fearing for his life, he gave information about Ms. Caruana Galizia’s murder in return for immunity and protection. He named Mr. Fenech as the paymaster and mastermind of the murder plot.

Mr. Fenech is part owner of companies that received a 450 million euro concession — almost $500 million — to build a controversial power plant that Ms. Caruana Galizia had written about extensively. She also wrote about a mysterious company called 17 Black that she believed was a conduit for kickbacks. After her death, Mr. Fenech was revealed to be the company’s owner.