The declaration came on Friday as hundreds of people defied a ban on rallying at a shrine to the first revolt in 1986 and the military barricaded its camps to keep troops from joining in.
Rumours of an attempted coup to overthrow Arroyo have been growing ahead of this week's anniversary of the "people power" revolt that ended the rule of former dictator Ferdinand Marcos in 1986.
General Generoso Senga, the chief of staff of the armed forces, said that Brigadier-General Danilo Lim, the commander of the Philippine Army's elite Scout Rangers, had been taken into custody on Friday.
Lim and another senior officer are being detained as alleged leaders of "misguided elements who were planning to join a march," against Arroyo on Friday.
"We believe that we have quashed a coup"
Lieutenant-General Hermogenes Esperon
"We believe that we have quashed a coup," Lieutenant-General Hermogenes Esperon, the army chief, said in an interview on an early morning television news programme.
Arroyo convened an emergency cabinet meeting before dawn and ordered presidential palace security to evict all reporters from the palace compound, according to journalists at the scene.
Opposition forces gathered at the rallying point for two earlier revolts by late Friday morning, calling for Arroyo, who survived allegations of vote-rigging and corruption last year, to step down.
On Thursday, military officials linked Gregorio Honasan, a former army colonel and opposition senator, hailed as a hero in the uprising against Marcos, to a fresh plot to unseat Arroyo.
Army officials said Honasan was recruiting junior officers to take part in "Oplan Hackle", which was uncovered this month by troops loyal to the president.
In interviews on Wednesday, Honasan said the government was spreading rumours about his involvement in a coup.
"Oplan Hackle" was meant to create a military government and involved the mass escape of officers facing trial for leading a failed mutiny in July 2003, an army official had said on Wednesday, adding the army had questioned at least 14 lieutenants and sergeants.
Arroyo survived the July 2003 military mutiny by around 200 soldiers in Manila, but has since been politically weakened despite shaking off an impeachment complaint lodged against her in parliament last year over opposition claims she stole the May 2004 presidential election.
A military-backed popular revolt that ousted Marcos in 1986 precipitated a string of bloody but failed coup attempts against his successor, Corazon Aquino.