He pleaded not guilty to the charge, and four others including membership of a criminal gang. Relatives of the assassinated blogger were present in the court in Valletta.
The investigation into Caruana Galizia's death has rocked the island's government. There is pressure on Prime Minister Joseph Muscat to resign over the issue.
His chief aide, Keith Schembri, quit this week amid reports he was being questioned by police, while Tourism Minister Konrad Mizzi also resigned and Economy Minister Chris Cardona took the decision to suspend himself.
Three people are awaiting trial for Caruana Galizia's murder in a car bombing but the police investigation is now focusing on who ordered the killing and why.
Fenech, a Maltese business tycoon, has been repeatedly questioned over the killing since trying to leave the island on his yacht on 20 November, and sought a pardon in return for providing information but his request was rejected.
Maltese media allege he was familiar with Melvin Theuma, a taxi driver with links to criminal enterprises who has been described in local media as a potential "middleman" in the murder.
Fenech is a well-known figure in Malta who has served as head of the Tumas business group and a director of energy company Electrogas but recently resigned from both positions.
He was identified last year as being the owner of a mysterious Dubai-registered company, 17 Black.
The company was listed in the Panama Papers - confidential documents leaked from a Panamanian law firm in 2016 which revealed how the wealthy and powerful use tax havens to get around the law.
Caruana Galizia had written about 17 Black eight months before her death, alleging it had links to both Keith Schembri and Konrad Mizzi.
( With inputs from IANS )