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.
