According to the National Historical Commission of the Philippines, Fonacier's public service at the university, which spanned more than six decades, is the longest on record in that country.
He served as Acting Executive Vice President of the university from 1956 to 1958, Dean of the College of Liberal Arts from 1963 to 1966, and as a member of the Board of Regents from 1966.
[6] By this time, then UP President Carlos P. Romulo appointed Fonacier as the first executive director of the Office of Alumni Relations.
While in this position, he and his managing editor, Leopoldo Yabes, faced a Supreme Court case in 1961 due to the publishing of the article entitled Peasant War in the Philippines in 1958.
By this time, the communist rebellion led by the Hukbalahap had already weakened, but remained a potential threat to the Philippine government.
The court ruled in favor of Fonacier and Yabes on the grounds that the prosecutor could not provide ample evidence of the defendants' seditious intent.
[citation needed] However, suspicion of Fonacier, despite his background as a pensionado in the United States, continued through the early years of the Marcos administration, when student movements such as the Diliman Commune in the University of the Philippines intensified, and there was a resurgence in the communist rebellion, this time led by the New People's Army.
On July 5, 1981, Fonacier died due to pneumonia at the Veterans Memorial Medical Center in Quezon City.