The Federal Emergency Management Agency said it had approved an extension of the Army Corps' oversight of more than 700 emergency generators across the island, including "the lease, generation and maintenance" of three "mega generators."
But the rebuilding of Puerto Rico's unreliable electrical grid, including restoring fallen power lines, will now be handled by the cash-strapped Puerto Rico Electric Power Authority, according to statement from FEMA.
The extension of the engineering corps' operation of emergency generators came at the request of the island's government, FEMA said.
Though the island's utility company on Wednesday reported that about 95% of its customers had power, at least 13,870 customers were still in the dark following the worst blackout in US history.
The hurricane, the strongest to hit the US territory since the 1920s, left nearly 1.4 million customers without power. But the federal government said the Corps' work is done and that the power authority will assume oversight of contractors completing grid restoration efforts
"If there are over 20,000 Puerto Rican-American citizens still without power, is your mission really accomplished?" New Mexico Sen. Martin Heinrich asked.
"Our mission, as assigned by FEMA, is," Alexander said.
"I cannot imagine a scenario where twenty-plus-thousand Texans or twenty-plus-thousand Floridians, were without power and FEMA would make that decision," Heinrich said. "I think that's reprehensible."
Alexander later told lawmakers: "We run out of money on the 18th and we run out of authority. ... I would be remiss if I didn't say ... it's not in our culture to walk away from a mission when it hasn't been fully accomplished. But we follow orders."
Puerto Rico's representative in Congress, Jenniffer Gonzalez Colon, had requested continued government support as the island struggles to restore power before the next hurricane season starts next month.
"The federal support for Puerto Rico power restoration must continue until full completion," Colon tweeted this week, calling the Corps' pullout "alarming." She said there are still 20,000 homes without service, mostly in remote rural communities.
The fragility of the grid was evident last month when most of the island was left without power
after an subcontractor's excavator steered too close to an energized line and an electrical ground fault caused a massive blackout.
Puerto Rico, home to more than 3 million US citizens, has grappled with widespread power outages for months since the storm.
Since the monster storm slammed into Caribbean territory in September more than 3.4 billion hours of electricity have been lost there, according to a recent report.
That makes it the second-longest blackout in world history,
according to a report from the Rhodium Group, an economic research firm.
The blackout is already the worst in US history, beating out Hurricane Georges in 1998 and Hurricane Sandy in 2012.
The only blackout in world history bigger than Puerto Rico's is the one that came after Typhoon Haiyan devastated the Philippines in 2013. About 6.1 billion hours of power were lost after that massive storm.
Puerto Rico's power authority faced widespread criticism late last year for signing a $300 million contract to restore power with Whitefish Energy Holdings, a small Montana-based firm with only two employees at the time.
The utility canceled the contract amid public outcry, and its executive director stepped down in November.
The Atlantic hurricane season lasts from June through November. This season could be a slightly above average one, according to a preliminary forecast.