A military spokesman said troops were placed on 24-hour standby with all leave canceled because of fears of communist guerrilla attacks, after exiled rebel leaders called for "widespread dissent" against the government.
The Communist Party of the Philippines called for Arroyo's removal through "a popular uprising, a civil disobedience movement, a mass withdrawal of support by political parties and personages, a voluntary resignation of Arroyo, a coup d'etat or any combination thereof".
At least three officers led by Major General Carlos Garcia, the former military comptroller, face possible court-martial for corruption for having unexplained wealth.
The probe was triggered by a tip-off from the US government early this year that Garcia and members of his family had brought nearly a million dollars to the United States over 10 years while he was earning about 7,200 dollars a year.
The Philippines suffered numerous coup attempts in the late 1980s.
Arroyo survived a military revolt last year after taking power in a military-backed popular revolt that ousted president Joseph Estrada in January
She has ordered the military to launch a court-martial against Garcia by Friday.
On Monday she said the scandal might provoke attempts to destabilize her government by entities other than guerrillas.
"I will deal with these destabilizers with an iron fist, even as I hold out an open hand and open mind for those who are open to a just and dignified reconciliation," she added.
The armed forces have "increased the troops' alert status to Red Alert effective 8:00 am today," military spokesman Lieutenant-Colonel Daniel Lucero said in a statement.
"This is to prepare the troops in the light of possible heightened attacks by the communist terrorists," the statement said.
Lucero told AFP the military warned two weeks ago that the guerrillas plan to exploit the present controversy,"
Earlier Tuesday another military spokesman, Lieutenant-General Edilberto Adan, angrily rejected a legislator's suggestions that its top brass was like a "Mafia" crime family.
Senator Miriam Santiago, in a speech on the senate floor on Monday, denounced what she described as massive plundering of military funds by its top 12 officers who she alleged acted like "the military Mafia, the military mob".
The comments were "an insult to the generals and the officer corps as well as to ordinary soldiers", Adan said.
Arroyo urged politicians to temper their criticism of the military, saying the government was already working to bring those guilty of graft to justice.
Filipinos should "not drench the uniform in dishonor for the wayward acts of a few," she added.
Communist guerrilla spokesman Gregorio Rosal said in a statement that Arroyo was "ripe for the ousting" for 10 reasons, including her alleged plan to terminate stalled peace talks with them.
Arroyo last week called for a review of the approach to the 35 year-old communist rebellion, citing what she described as growing links between the rebels and unidentified international terrorist organizations.