On Thursday, the jury in the trial unanimously concluded that prosecutors had failed to prove the defendants' guilt and all three were released in the courtroom.
Novaya Gazeta reporter Politkovskaya, who gained international recognition for her reports of atrocities against civilians in the troubled Caucasus republic of Chechnya, was gunned down in an elevator in her Moscow apartment building in October 2006, in what police described as a contract killing.
Dzhabrail and Ibragim Makhmudov, brothers from Chechnya, and former police officer Sergei Khadzhikurbanov were charged with involvement in the murder. A former Federal Security Service (FSB) officer, Colonel Pavel Ryaguzov, has also been charged with telling the killers where Politkovskaya lived.
Judge Yevgeny Zubov ruled that the case be referred back to an investigative committee at the Russian Prosecutor General's Office and said that the verdict could be appealed within a 10-day period.
The Moscow Military District Court also granted the acquitted the right to file civil suits demanding compensation for ungrounded judicial persecution.
At the same time, the court left a claim by Politkovskaya's children for 10 million rubles ($276,650) in compensation unconsidered.
"I consider that the people who were acquitted today were involved in my mother's murder. However, I respect the jury's verdict. It was important that it was unanimous. If I am disappointed in anything, then it is in the investigation into the case," Novaya Gazeta quoted Politkovskaya's son, Ilya, as saying on Thursday after the announcement of the verdict.
His words were echoed by Novaya Gazeta chief editor Sergei Sokolov, who also criticized the investigators' work, pointing out that they had not even taken a computer from Ryaguzov's apartment.
"We insist on the guilt of the accused. The investigation was categorically not allowed to work. The entire corrupt law enforcement system stood against it. It is obvious that they wanted to save their own people who were mixed up in this case," he said at a news conference in Moscow on Thursday.
"You can consider that a verdict was brought today against the country's entire law enforcement system. It is rotten right through," he said.
Lawyers for Politkovskaya's relatives said earlier they would seek another investigation.
"We want the real killer [in the dock], and we will succeed," lawyer Karina Moskalenko said, but declined to give an opinion on the verdict, saying it was "neither good nor bad."
London-based human rights organization Amnesty International called on the Russian authorities to carry on with the investigation and to find the real organizers and perpetrators of the murder.
"We urge the relevant Russian authorities not to stop here but to continue the investigation into the murder and to bring to justice all those involved, including the gunman and those who ordered the killing," the organization's official website quoted Europe and Central Asia Program Director Nicola Duckworth as saying.
She added that the end of the trial does not mean that the Russian authorities are no longer responsible for finding the murderer and his 'sponsors.'
"Delivering justice for the murder of Anna Politkovskaya will demonstrate that the Russian authorities have the political will to end the silencing of human rights defenders," Duckworth said.
Following the jury's decision, the OSCE Representative on Freedom of the Media Miklos Haraszti immediately accused Russia of total ineffectiveness in protecting its journalists.
"The Politkovskaya verdict tops the long history of inability of Russia's authorities to provide safety to embattled journalists. This amounts to a practical impunity for the murder and physical assault of those covering corruption and human rights issues," he said.
"There can be no true freedom of the press as long as the brightest journalists across the country fear being killed for doing their job," he said.
Since the collapse of the Soviet Union in 1991, Russia has been one of the most dangerous countries for reporters. Around 50 media professionals have been killed in Russia since 1992. Only Iraq and Algeria have had more deaths over that time.
Just last month, Novaya Gazeta journalist Anastasia Baburova was shot dead alongside lawyer Stanislav Markelov in downtown Moscow.
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Some people are trying to make the reality in Russia at least a bit more humane. The amnesty should apply not only to persons involved in high-profile cases, but also to individuals who are not as well-known. It is better to set free at least some of the individuals who deserve to be released than no one at all.