Gregg Jones' excellent article, "Philippine Province Ruled by Renegade" {front page, Sept. 12}, highlights a serious danger -- the Balkanization of the Philippine military -- now confronting the Aquino government. Col. Rodolfo Aguinaldo's rebellion, in Cagayan province, the home base of former defense minister Jose Enrile, came as no surprise, however, to those who have met the enigmatic colonel.

I had that opportunity when I visited Cagayan province to observe the February 1987 constitutional plebiscite. On the eve of the plebiscite, I went with two U.S. Embassy officials to the home of a local politician closely aligned with Mr. Enrile. We were soon joined by Col. Aguinaldo, whose exploits in combating the insurgents had been acclaimed by many, but who had also been criticized by those sensitive to human rights concerns.

For the next three hours, we heard "the world according to Aguinaldo." He expressed contempt for civilian government and criticized President Corazon Aquino, Gen. Fidel Ramos and the U.S. government for failing to see the dangers posed by the New People's Army. He admitted to campaigning for a "no" vote in the plebiscite on the grounds that the constitution would weaken the military.

Most chillingly, Col. Aguinaldo explained that the previous week's coup was the work of amateurs; he predicted a "real" coup within the next several months, led by those officers, including himself, who had been involved in ousting Ferdinand Marcos. Finally, he indicated he would resist any attempts to remove or reassign him -- threatening to go into the mountains with his men if neces-sary.

I returned to Manila shellshocked. My Filipino friends acknowledged Col. Aguinaldo as a bad apple, but did not believe his attitude posed a serious threat to the regime. It now appears, though, that his remarks that February night were more than just bluster. Since I assume I was not the only one who had an opportunity to hear his views, one wonders why he is allowed to remain as a provincial commander.

Col. Aguinaldo's views are one of the tragic legacies of the Marcos regime and pose a major challenge to the Aquino government. Soldiers like Col. Aguinaldo believe they know what is best for the Philippines and are not willing to subject themselves to the authority of the democratically elected government. In combating this challenge, President Aquino must ensure that the military, particularly the officers being trained today, understand the role of a military in a constitutional government. Failure to establish the authority of the civilian government inevitably will lead to more serious problems. LARRY GARBER Acting Director International Human Rights Law Group Washington