Earlier this year, the country's supreme court sentenced Pollycarpus Budihari Priyanto, a Garuda pilot, to 20 years in jail for his part in Munir's murder.
Indra Setiawan, a former airline official, received a one-year sentence for being an accessory.
Muchdi is the first official from the country's intelligence agency to be linked to a plot to kill Munir, and whose involvement could implicate others.
Munir made many enemies among Indonesia's powerful for exposing abuses by the army in East Timor and Papua during the US-backed rule of Suharto, the former president.
On Thursday the prosecution said the ex-spy had "ordered Munir be killed" because he had exposed Muchdi's involvement in the abduction of 13 activists that led to his sacking.
"The defendant is charged for acting alone or together with Pollycarpus conducting a premeditated murder of human rights activist Munir during a flight from Jakarta to Den Haag," Silu told the court.
Lutfi Hakim, the defence lawyer, dismissed the accusation as "absurd".
An independent fact-finding team established by Indonesia's president revealed phone records showing calls between Pollycarpus and a phone registered to Muchdi before the murder.
At the pilot's trial, Muchdi testified that someone borrowed his telephone to make the calls.
The case is seen as a test of the government's determination to uphold the rule of law, as well as the accountability of several state agencies.