Brothers George and Alfred Degiorgio, aged 55 and 53, and Vincent Muscat, 55, all pleaded not guilty.
They were also accused of possession of bomb-making material and weapons.
Caruana Galizia died in an explosion shortly after she left her home in Bidnija, near Mosta, on 16 October.
The 53-year-old was known for her blog accusing top politicians of corruption.
On Monday, police arrested 10 Maltese nationals in connection with the murder. Police operations took place in the town of Marsa, and the Bugibba and Zebbug areas.
Prime Minister Joseph Muscat, who is not related to Vincent Muscat, said some of the 10 detainees were already known to the police while others had criminal records.
The Times of Malta reports that the three men who have been charged were among those arrested.
A close friend of Caruana Galizia told Reuters news agency that she did not think the journalist had ever investigated the men.
The government had offered a $1.7m (€1m) reward for information about Caruana Galizia's murder.
Her three sons refused to endorse the reward, and said they were "not interested in justice without change".
In her Running Commentary blog, she had relentlessly reported on alleged corruption among politicians across party lines.
With a career spanning more than three decades, she was "one of Malta's most important, visible, fearless journalists", in the words of former Home Affairs Minister Louis Galea.
Her funeral was attended by hundreds of people but the tiny EU state's leaders were barred by her family.
International experts, including from the FBI, were called in to help in the investigation.
The editors of eight of the world's largest news organisations, including the BBC, called for the European Commission - the EU executive - to investigate the murder.
In response, Frans Timmermans, vice-president of the commission, urged the authorities to leave "no stone unturned" in the case.
Photo: supplied Daphne Caruana Galizia