Ramon Cardenas, who was Estrada's political adviser, was arrested following a raid on his home in the Philippine capital Manila.
Cardenas’ home is near a residential and commercial building the mutineers had taken over before surrendering late Sunday, according to AFP reports.
Police said they had also seized military uniforms and other materials from Cardenas' home. These reportedly included red armbands similar to those worn by the mutineers.
Interior Secretary Jose Lina said earlier on Monday the military officers had not acted on their own but had received backing from political figures close to Estrada.
Evidence was also being gathered against another key Estrada ally, opposition senator Gregorio Honasan, who in the late 1980s led several coup attempts against the government.
The Philippine Star newspaper quoted Arroyo as saying that civilians found to be conspiring with the military officers in staging the aborted coup would be prosecuted.
Mutineers trapped Australian amassador
The 296 mutineers, who seized the building in Manila’s business and entertainment district of Mikati on Sunday, accused Arroyo of corruption and demanded she step down.
Under pressure: President to
address the nation on Monday
Several foreigners, including the Australian ambassador, were briefly trapped inside.
But after a 22-hour standoff with pro-government forces, the coup plotters surrendered under threat of force and agreed to return to barracks.
Arroyo, who has promised to bring to justice everyone involved in the failed uprising, is due to give her State of the Nation address in parliament later on Monday. She is expected to refer to the incident.
Estrada is in custody and on trial for corruption, but he was seen as a champion of the poor. Arroyo's rule has been dogged by uncertain popularity and weak economic growth.
The Philippine Star quoted economic analysts and business leaders who warned the mutiny would “drive away investors and leave the country’s near-term economic prospects in tatters.”