A Moscow jury acquitted the defendants -- two Chechen brothers and a former policeman
-- in February after a trial that Politkovskaya's supporters said was undermined by prosecution errors.
The prosecutors appealed, accusing the judge of making numerous procedural violations.
The Supreme Court agreed there had been a violation of procedural rules, court spokesman Pavel Odintsov said. The court ordered a new jury trial.
Not guilty verdicts are often reversed by Russia's higher courts.
All three defendants were accused of playing minor roles in the shooting death of Politkovskaya in 2006. Prosecutors never explained who might have ordered the suspected contract killing, and the suspected gunman remains at large.
Karinna Moskalenko, a prominent lawyer who represents Politkovskaya's family, said it was important for the investigators to do a better job making their case the second time around.
"We have hope," she said. "What they did before was unsatisfactory. The children still have hope."
Defense lawyer Murad Musayev said he had expected Thursday's decision.
"I'm convinced that if a new court is able to look at the process objectively and properly then our arguments will again be upheld," he said.
Politkovskaya was a ferocious critic of former president and current Prime Minister Vladimir Putin. She also angered officials with her persistent reporting of human rights abuses and corruption in Chechnya, under the leadership of Kremlin favorite Ramzan Kadyrov.
Her killing deepened international concerns about the risks journalists and Kremlin critics face in Russia, and added to strains in ties with the West.
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