The tree, which came down on the line in mountainous Cayey, also cut power supply to the light rail train. The agency said it had restored power to 30,000 clients.
"A fallen tree on line 50900 in high Cayey disrupted energy supply from Manatee to Yabucoa. We continue efforts to restore power to about 840,000 customers," it tweeted.
The authority estimated it would take between seven and 11 hours to restore power. NBC News reported that the biggest hospital in San Juan, the capital of the US territory, was running on generators.