Prosecutors said Ramon Cardenas, head of the presidential management staff during the Estrada administration, allowed a home he owned to be used as a "staging point" for the rebellion.
In its charge sheet filed on Tuesday before the Makati Regional Trial Court, the prosecutors said Cardenas "may be considered as a promoter or maintainer of the rebellion".
Cardenas was detained on Monday after police said they found weapons, ammunition and red armbands used by the rebel soldiers in his house.
His lawyer told reporters the evidence was planted by the police and Cardenas would strongly contest the charge. Estrada, who is being held in a military hospital while on trial for economic plunder that is punishable by death or life in prison, has denied involvement in the mutiny.
As the country debates the significance of the weekend’s failed revolt, officials said on Tuesday the coup leaders included US-trained bomb-making experts who were backed by political forces.
The day-long uprising by junior officers, who accused President Gloria Arroyo of corruption as well as weakness in dealing with Muslim separatists, ended without bloodshed on Sunday.
Arroyo has vowed to address the grievances. But accusations are flying that the mutiny could not have been staged without the support of some of her political foes.
In an action supporting that thesis, an aide to former President Joseph Estrada, Ramon Cardenas, was arrested on Monday in connection with the mutiny.
Parallels are also being drawn between Arroyo and Corazon Aquino - whose 1986-1992 presidency was marked by economically crippling coup attempts - as two leaders swept into power pledging to stamp out corruption but failing to do so.
Joel Rocamora, head of the Institute for Popular Democracy think-tank, told Reuters the latest mutiny had no public support and that Arroyo's opponents would be weakened by any association with the renegade soldiers.
"If the president is perceived to have followed through on the government's promise to carefully consider the issues raised by the young officers, Gloria might actually come out of this ahead," he said.
"Are there likely to be more coups like this? I doubt it."
Rebel officers trained by US special forces
But unlike most previous military coup attempts in the Philippines which were backed by heavy artillery and ground-attack aircraft, Sunday’s mutineers used "dangerous explosives" as their "weapon and bargaining chip," a security official said.
"If they had used the explosives, the potential for destruction of a key part of the Makati financial centre was enormous," the official told AFP. "But I don't think they had cold-blooded intentions although they were hot-headed young officers."
Politician Ramon Cardenas (C)
was detained after Sunday's siege
Four of the leaders who led a 300-strong force in a standoff with pro-government troops in Manila's financial district had received anti-terrorist training from US special forces last year.
They underwent sniper training, night fighting as well as counter-terrorist tactics in the southern Philippines, said a senior military official, who asked not to be named.
The military rebels had assembled powerful C4 and TNT explosives at strategic points around the shopping and apartment complex in Makati in the early hours of Sunday before challenging the security forces to face them.
Defence Secretary Angelo Reyes on Tuesday presented documents showing expensive communications equipment was shipped into the country by a political group he claimed had links to the soldiers.
"These are expensive communications and supplies which are not regular supplies of the armed forces," Arroyo's spokesman Ignacio Bunye was quoted by AFP as saying.