But Karinna Moskalenko, a lawyer for the family, said satisfaction would depend on the extent of prosecutors' co-operation on the case.
"Why should we be fully satisfied if three years have passed and the case has practically not been properly investigated," she said.
"We were denied access to the investigation. Now let's see to what extent they [prosecutors] are ready to co-operate."
Politkovskaya, a 48-year-old mother of two who published damning exposes of official corruption and rights abuses, was shot dead in the stairwell of her Moscow apartment on October 7 three years ago.
The new ruling will apparently end the retrial of three suspects whose acquittal was overturned by the supreme court earlier this year.
The three are accused of helping set up the slaying, but not of shooting the journalist or planning her death.
In Thursday's ruling, the court's military branch ordered their case to be merged with that against Rustam Makhmudov, the suspected gunman, and efforts to determine who was behind the contract-style killing.
The ruling could increase chances that authorities will eventually determine who was behind Politkovskaya's murder, a crucial question in a country plagued by killings of journalists and activists.
During her career, Politkovskaya sharply criticised Vladimir Putin, the president at the time, and the Kremlin-backed government of Chechnya.
The southern Russian area was the site of two post-Soviet separatist wars and of widespread rights abuses that Politkovskaya focused much of her investigative reporting on.