But a summary of their ruling said there was insufficient evidence to show that he "had a conscious and close co-operation with those in the Philippines who carried out the deed".
Sison had denied ordering the separate killings of two former political associates in Manila. He also denied the attempted murders of two other people.
Wim de Bruin, prosecution spokesman, said that they planned to appeal against the decision to release Sison.
"In the meantime, the investigation will continue, and Mr Sison remains a suspect," he said.
|"In the meantime, the investigation will continue, and Mr Sison remains a suspect"|
Wim de Bruin, prosecution spokesman
The Communist Party issued statement claiming it carried out the killings of Romulo Kintanar, who was shot dead in a restaurant in 2003, and Arturo Tabara, who was killed along with with his son-in-law in 2004.
Both had separated from the New People's Army (NPA), the military wing of the party which has been fighting the Philippines government across the archipelago for nearly 40 years. More than 40,000 people have been killed in the violence.
"We're very happy Joma has been released now after 15-16 days of solitary confinement," Luis Jalandoni, a close aide to Sison, said, referring to him by his nickname.
"We are thankful to his lawyers, who worked very hard for his release."
Gloria Macapagal Arroyo, Philippine president, has said she sees the NPA as the country's most serious security threat and last year declared all-out war on the rebels.
Peace talks between the two sides collapsed in 2004 when Washington and some European states put the group on their terrorism blacklists.
Last month, the European Union's highest court annulled a decision by the bloc to put Sison on its terrorism list.