General Fortunato Abat described his action as peaceful takeover, even as he called on police and military forces to withdraw support from President Arroyo and "protect the sovereign right of the people."
The 80-year-old retired general made the announcement before an audience of about 300 people at the Club Filipino in the municipality of San Juan, in Metro Manila.
Arroyo, attending a summit of the 10-nation Association of Southeast Asian Nations in Kuala Lumpur, has been haunted by a monthslong drive to remove her from power, and coup rumors rose to a new crescendo in the days before her departure Sunday.
Addressing a news conference in Kuala Lumpur, the President declined to comment on the reported coup plot.
But security officials in Manila dismissed the supposed military takeover as "blind rumors" even as Philippine police chief General Arturo Lomibao on Tuesday placed police forces on a full alert status, convened the crisis committee, and directed the intelligence services to validate the reports.
Armed Forces Chief of Staff General Generoso Senga said the soldiers remained loyal to the Constitution and the chain of command.
Abat, a former Army chief and defense secretary, is convener of the right-wing Coalition for National Solidarity which has been calling on Arroyo to step down.
When the wiretaps scandal broke out in June, Abat called for the establishment of a civilian-military junta and offered himself to head it.
The 117,000-strong military has a history of unrest and played key roles in the ouster of dictator Ferdinand Marcos in 1986 and jailed former president Joseph Estrada in January 2001.
Two years ago, about 300 soldiers, led by young officers, occupied the ritzy Oakwood Hotel and a nearby shopping mall in the capital's financial district and rigged the area with bombs. They surrendered peacefully after about 20 hours.
The coup rumors have been swirling since June, when vote-rigging allegations against Arroyo prompted several cabinet members to resign and key political allies and left-wing groups to call for her resignation.
She survived an impeachment attempt in September when her majority allies in the House of Representatives junked three impeachment bids on a technicality. Opponents continue to call for her resignation and hold occasional small street protests.