Puerto Rican officials had warned on Friday that they would not make the payment because the island legislature failed to appropriate the funds, but they argued it should not be considered a default.
Moody's Investor Service said the missed payment was the first in what it believes will be broad defaults on commonwealth debt.
Government Development Bank President Melba Acosta Febo said Monday that Puerto Rico made a partial payment of $628,000 interest.
Gov. Alejandro Garcia Padilla said several weeks ago that Puerto Rico cannot pay its $72 billion in accumulated public debt and needs to restructure.