They say Pollycarpus, a former pilot with the national airline Garuda, poisoned Munir during his flight from Indonesia to the Netherlands.
In December 2005 Pollycarpus, who was on the flight but not on duty, was found guilty of the murder.
But his conviction was quashed by the Supreme Court in October 2006.
|Pollycarpus denies any involvement |
in Munir's death [Reuters]
He has always denied any involvement in Munir's death.
Munir was Indonesia's most prominent human rights activist and founded the group Kontras.
He often targeted the country's powerful military and secret service.
He died from arsenic poisoning while on a Garuda Airlines flight to the Netherlands in September 2004.
Now, for the first time, the police have offered evidence to the court about the involvement of the national intelligence agency in his high-profile murder.
It could be the first step to unravel a sensitive case.
"Now is the time to really punish those who are really behind this murder"
According to the prosecutors, Munir was poisoned at a coffee shop during transit in Singapore.
A witness saw Pollycarpus giving him a drink.
Indra Setiawan, the former director of Garuda, has declared that he signed a letter from the intelligence agency giving Pollycarpus a special assignment.
His lawyer, Antawirya, says he did not know Munir would be murdered. The letter has since been stolen.
"This was an official letter with the letterhead of the Intelligence Agency asking the Garuda director to assign pilot Pollycarpus as part of the aviation security," Antawirya told Al Jazeera.
In the documents that have been handed over to the court, an intelligence agent declares that he was ordered to kill Munir months before he died.
|Rights groups say Munir's killers must |
be brought to account [EPA]
One section reads: "Agent Raden Anwar of the intelligence agency together with agent Sentot got the instruction from his superior to kill Munir. But this plan failed."
Another paragraph reads: "After it is known that Munir had died, Raden Anwar called agent Sentot and asked about his death, the agent said this is not our business, this is the business of our boss."
Munir's widow, Suciwati, and supporters say they are now optimistic that with this evidence the real conspiracy behind his murder can be revealed.
"Now is the time to really punish those who are really behind this murder," Suciwati told Al Jazeera. "Only then Indonesia will be respected in the world."
"This is the right time for Indonesia’s democracy to reform intelligence, this has to be done today, now, or never"
Munir family friend
Usman Hamid, a family friend, says the case offers a one-off chance to bring the intelligence services to account.
"The intelligence agency has never been touched by a legal process," he said.
"This is the right time for Indonesia's democracy to reform intelligence, this has to be done today, now, or never."
The intelligence agency has denied any involvement in Munir's murder.
Now it is up to the court to decide if the evidence is strong enough to reopen the case.