The manhunt for Lieutenant Colonel Oscarlito Mapalo comes amid an anti-corruption crackdown on the armed forces, which has triggered fears of renewed destabilization attempts by an institution that has mounted eight failed mutinies, the latest one against President Gloria Arroyo last year.
Mapalo was restricted to quarters in September for publicly denouncing the institution's promotion system as biased and lacking in objectivity.
He left his quarters without permission early last week and has not reported back, military spokesman Lieutenant Colonel Buenaventura Pascual told reporters.
Armed Forces chief of staff General Efren Abu has ordered the arrest of Mapalo, Pascual added.
Last week, Mapalo and Colonel Jose Gamus, were investigated for alleged involvement in a destabilization plot against Arroyo.
The supposed plot had been timed to coincide with the December 22 burial of movie star Fernando Poe, who narrowly lost to Arroyo in the May presidential election, the military has alleged.
Neither officer has been charged and the funeral went ahead without incident.
"Days before the burial, there were reports of destabilization (plots) involving Lieutenant Colonel Mapalo. It was bolstered by his escape the day before (the burial)," Pascual said.
Arroyo crushed a bloodless mutiny by several hundred elite troops last year and has since pledged reforms.
The military's former top finance officer is being court-martialled for alleged corruption.