Gen. Telmo Sandoval, head of the joint chiefs of staff, Vice Adm. Enrique Monteverde, head of the navy, and air force Gen. Ricardo Irgoyen presented their resignations to President Gustavo Noboa on Monday, a government news release said without providing further details.
Defense Minister Hugo Unda told reporters that Noboa was considering candidates to replace the top military commanders, but refused to elaborate. Noboa assumed the reigns of government after President Jamil Mahuad was ousted on Jan. 21 by a military-backed uprising.
The news came as Congress started debate on Noboa's request to offer amnesty to military officers involved in January's aborted coup.
Political scientist Simon Pachano said the resignations of top military leaders and the offer of general amnesty was a step toward ending divisions within the military and repairing its damaged image.
Mahuad was forced from power after hundreds of Indian protesters, backed by a cadre of young army officers, occupied the empty Congress building and proclaimed a "Parliament of the People."
The military high command refused to put down the insurrection and forced Mahuad from power to avoid "a social explosion."
Former armed forces chief Gen. Carlos Mendoza, who had joined the junta, turned power over to Noboa, Mahuad's vice president, under pressure from the U.S. State Department and at least 20 regional commanders who opposed the overthrow of civilian rule.
Missing from the resignation list Tuesday was Gen. Norton Narvaez, commander of Ecuador's ground forces, who joined the military high command after the rebellion and was widely perceived as not involved in Mahuad's ouster.
Military tribunals are trying 17 military officers, most of them colonels, for their part in Mahuad's unconstitutional ouster.
Mendoza, who resigned his post, said later that he agreed to join the coup as a stall tactic until democratic order could be restored.
Ecuador's high military tribunal is considering whether to pursue charges against Mendoza and dozens of other officers for possible court martials.
Some political parties, including the influential Social Christians, oppose a general amnesty, but Ecuador's powerful Indian movement has demanded that its allies in the military be cleared of all charges.