“We’re standing firm,” he said, in comments translated and disseminated through a messaging application by a team from the newspaper.
The four who remain detained are Mr. Atalay; Murat Sabuncu, the editor in chief; Kadri Gursel, a senior columnist and adviser to the board; and Ahmet Sik, an outspoken investigative reporter.
They are charged with aiding several terrorist groups and having an editorial policy that favored the groups. In their defense, the journalists and managers said during the hearings that they had had minimal contact with suspects and only in the course of their journalistic work.
“This verdict here today says, ‘We will make you kneel,’” Mr. Sik called out to colleagues and reporters. “Up until today I only bow my head to kiss the hands of my Mum and Dad, and it will be the same after today.”
The decision was more or less expected, and was greeted with mixed feelings by family members and colleagues.
“We will keep working until we get them all back,” Elif Gunay, the daughter of one of the released defendants, wrote on the same messaging application.
But a senior columnist, Aydin Engin, who has been running the newspaper since their arrests, said it would be a struggle for the paper to survive. “It is very difficult to go on” without those “key people,” he said. “For nine months I was trying to take on their responsibilities, but I am 76 and it is very difficult.”
Mr. Atalay in his testimony on Monday accused the government of President Recep Tayyip Erdogan of trying to silence the paper or seize control of it. And he challenged the very premise of the trial. One of the main charges is that he and his colleagues had changed the editorial direction of the newspaper, which, he said bluntly, the court had no business to question.
Cumhuriyet, founded 93 years ago, is the oldest daily newspaper in Turkey, and nearly as old as the republic itself. Run by a foundation, it has a strong reputation of independent reporting, and its reporters and columnists have been in prison many times over the years for breaking government or military taboos.
Turkey was notorious for being the world’s leading jailer of journalists in the 1990s, but for a decade that began in 1998 the country and later Mr. Erdogan’s Justice and Development Party, or AKP, began reforming its ways. By 2008 only one journalist was behind bars.
In July 2008, though, the government accused a shadowy nationalist organization of plotting a coup and began a series of prosecutions that led Turkey once more to authoritarianism and media oppression. That has accelerated since the coup attempt in July 2016.
According to the Committee for Protection of Journalists, 81 journalists were imprisoned in Turkey in December 2016. The number today is at least 150, Mr. Sik said in his defense Wednesday.
Mr. Sik delivered an impassioned tirade, the written text of which was published by PEN International, against both the Fetullah Gulen movement, blamed for orchestrating last year’s failed coup, and Mr. Erdogan’s increasingly authoritarian government, which has arrested and suspended tens of thousands of plot suspects since the coup.
“This war is not for democracy and a clean society, nor for peace or civilization, as somebody claimed,” he said. “They are just fighting to be the owner of the state.”
The prosecutor lodged a complaint with the judge that Mr. Sik’s comments, far from a defense, represented a repetition of the crimes of which he is accused.
Mr. Sik pointed out that he had been imprisoned in 2011 for exposing the workings of the Gulen movement and its infiltration of state institutions, and now is being prosecuted for being allied with the movement.
A group of international organizations supporting freedom of expression and professional journalists, including PEN International and the International Press Institute, which monitored the trial, raised concerns that the Turkish authorities had failed to conduct a proper investigation and that the indictment relied on factual errors.
News reports were mischaracterized and prosecutors relied on experts whose qualifications seemed questionable, a group statement issued by the press institute said.
“This case should not have been brought and should be withdrawn fully and without delay,” it concluded.