Major Jason Aquino of the Army Scout Rangers was relieved as operations chief of the paratrooper unit on Sunday, his commanding officer Major General Hermogenes Esperon told reporters.
Aquino was sacked for "politicking" after it was found out that he was the source of a pamphlet being distributed to the ranks that openly questioned Arroyo's administration.
Aquino was "calling for a change in the political set-up," Esperon told reporters. "We deemed it proper to relieve him because his (position) ran contrary to his work as a military officer."
"He can entertain political thoughts, but he cannot do it while in office."
Major General Romeo Dominguez meanwhle quit his post as commanding general of the military's northern Luzon command, just two days after one of his men was linked to destabilization plots against Arroyo.
"The resignation is effective July 15 but was filed earlier to wait for a replacement," a military source said of Domingo's resignation.
The general was scheduled for retirement in October.
Arroyo has been accused of cheating in the May 2004 polls. She has apologized to the nation for improperly telephoning an election official but denied she rigged the vote.
The case has triggered street protests and caused the financial markets to tumble.
Senator Rodolfo Biazon, a former military chief, said Wednesday that a group of officers is considering quitting to protest allegations that Arroyo used the army intelligence unit in last year's polls.
Biazon, who ran under Arroyo's ticket last year, said a group of active-duty officers including several generals called on him on Saturday.
The officers were "hopping mad" over allegations that the administration used the military to steal the vote and asked him whether as a last resort they should file mass resignations.
Biazon said he counselled the group to stay put "because if they do this, this country will be thrown into chaos."
Arroyo survived a mutiny by several hundred soldiers who seized part of Manila's financial district in July 2003 to protest alleged government corruption.
The vote-cheating allegations arose from audiotapes of tapped telephone conversations that purportedly had Arroyo asking a top election official to guarantee her a million-vote winning margin.