The court in Silivri outside Istanbul ruled that 44 suspects -- including the self-confessed attacker Uzbek citizen Abdulkadir Masharipov -- must stay in jail.
But it said seven could go free under judicial control. This means that they remain charged and will have to regularly report to the authorities.
A total of 57 suspects are on trial, with the remaining number freed under judicial control or on the run.
The trial opened on December 11 with the court hearing five days of testimony. The next hearings will begin on March 26.
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The deadly attack on the Reina nightclub killed 39 people, most of them foreigners, who were celebrating the start of 2017.
Masharipov, who was captured after 17 days on the run, faces 40 life sentences, one for each of the victims and the massacre itself.
After taking a taxi to the elite waterside nightclub, Masharipov shot dead the security guard before marching inside and firing indiscriminately with his AK-47 at the terrified revellers and setting off grenades.