The resignation of Brigadier-General Victor Corpus was among the demands made by the mutinous junior officers who led a 19-hour uprising on Sunday.
But National Security Adviser Roilo Golez denied the departure of Corpus was in response to the soldiers' demands, Reuters reported. Golez told local television on Wednesday it had been considered for a month.
The resignation comes as Muslim separatists in the southern Philippines claimed they had bought weapons from the military, AFP reported. If true, this would confirm an allegation made by the mutineers.
“The current political crisis is far from finished,” Corpus said in his resignation letter to President Gloria Arroyo. “There is still deep restiveness in the Officers' Corp of the AFP (Armed Forces of the Philippines).”
Corpus was a promising army lieutenant when he defected to the communist New People's Army in 1970 in disgust over corruption during the rule of President Ferdinand Marcos. He led guerrilla bands against pro-Marcos forces before returning to the establishment 16 years later.
Army accused of prolonging rebellions
Meanwhile, rebels of the Moro Islamic Liberation Front (MILF), engaged in a 25-year insurgency in the south, said they had bought arms from the military.
But MILF spokesman Eid Kabalu told the AFP news agency there was no wholesale collusion between his separatist group and the army. He said it was likely that only individual solders were selling weapons to the guerrillas.
Filipino soldiers hunting rebels:
But are they arming them too?
The military denied the accusation but said it has ordered an inventory of all its weapons and ammunitions.
The officers who mutinied on Sunday accused Arroyo's government of selling weapons to the MILF, the communist New People's Army and the Abu Sayyaf kidnap gang.
They said the government had done so in an attempt to prolong the insurgencies and get more military and financial aid from the United States.
Enquiry probes backing for mutiny
The government has denied the accusation but Arroyo on Monday set up an enquiry to probe the claims.
Golez said investigators should explore who instigated and funded the ninth army uprising in the Philippines in 17 years. They should also study allegations that the mutineers planned to set up a 15-member ruling junta, he said.
“These guys did not act on their own. They appear to be well funded,” he said. “They were showing logistics and equipment that were not issued by the Armed Forces of the Philippines.”
Arroyo’s government is pointing the finger at supporters of former president Joseph Estrada, ousted by an army-backed popular revolt in 2001. Estrada has denied any involvement.
State prosecutors have filed rebellion charges against Ramon Cardenas, a member of Estrada's cabinet, for allegedly encouraging the mutiny. He denies the charges.