Politkovskaya, a writer of books and articles that fiercely criticised Vladimir Putin, the then Russian president, was shot dead in her central Moscow apartment building in October 2006.
Yevgeniy Zubov, a Russian judge, has sent the case back to Russian state prosecutors.
Zubov said: "The criminal probe must return to the prosecutors' investigative committee with the aim of finding the individuals linked to the committing of this crime."
Neave Barker, Al Jazeera's correspondent in Moscow, said: "There are those who criticised the whole trial process, saying that those people who are being accused in the first place had nothing to do with masterminding this whole thing and that the person who actually pulled the trigger was not up there behind the dock either.
"So there is the feeling that this whole process was very much a case of the authorities being seen to process this case.
"But, as we have seen with the results ... it does appear as if this verdict does mean that this case will undoubtedly continue in some shape or form in the future.
"This verdict does very little to provide confidence for the family and loved ones and colleagues of Anna Politkovskaya, who were hoping that the authorities might be able to provide a little bit more clout in bringing those who were actually involved in the killing to justice".
Elsa Vidal, from Reporters Without Borders, said the verdict was the "result of an incomplete investigation".
She told Al Jazeera it was important to "keep looking for the truth" in the case over Politkovskaya's murder.
"We have to rely on the impression that the family has on this topic, and so far they have said they were satisifed with the work of the investigation.
"What we are more doubtful about is the political will behind the investigation and the fact that there is a real commitment to finding the truth and bringing the mastermind in front of the court," she said.
Politkovskaya, who was 48 when she was killed, focussed her writing on abuses committed by Russian forces during the second Chechen war, which took place during Putin's presidency.
Her killing, as she returned home carrying bags of groceries from a shopping trip, sparked outrage internationally and among opposition groups in Russia, with some critics blaming the Russian leadership.
Many of her colleagues believe her murder was linked to her work reporting on abuses by Russian troops in Chechnya.