The government says the plot against Arroyo also included plans to kill her.
Among those charged are six leftist members of Congress, soldiers and communist rebels.
The congressmen have taken refuge in the House of Representatives since February in order to avoid arrest.
Philippines President Gloria Arroyo (Canadian Press)
Congressman Teodoro Casino, who has been charged, says they are being persecuted by political association.
"I am charged as a conspirator in ambushes that happened in 1969, in bombings that were supposedly launched by the New People's Army in 1970s," he said.
"I was only one or two years old at that time, so it is a shotgun approach, it's a sweeping accusation, and they could not even indicate what overt acts of rebellion were committed by the six of us legislators," said Casino.
The 52-page document filed in court alleges that the leftist lawmakers and communist leaders conspired with each other for more than a decade in planning a rebellion against the government.
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