By Akane Otani

Public works and utilities crews began restoring power to millions of households while New York's governor ordered an investigation into the state's utilities, a day after Tropical Storm Isaias downed trees and power lines throughout New York, New Jersey and Connecticut.

More than two million households across the region still don't have power, according to estimates provided by utilities in the three states. The storm also knocked out power for more than 200,000 customers served by Consolidated Edison Inc. in New York City and Westchester, causing one of the worst outages in its history, according to the utility.

New York Gov. Andrew Cuomo said Wednesday he was directing the state's Department of Public Service to investigate six utilities serving New Yorkers over the widespread power failures.

"We know that severe weather is our new reality, and the reckless disregard by utility companies to adequately plan for Tropical Storm Isaias left tens of thousands of customers in the dark, literally and figuratively," Mr. Cuomo said in a statement. "Their performance was unacceptable."

Mr. Cuomo added that utilities had deployed 7,000 workers working around the clock to repair damage from the storm.

Isaias wound up being "one of the most serious weather events since Hurricane Sandy," said New York City Mayor Bill de Blasio on Wednesday.

Although the storm was relatively brief, with the bulk of its impact passing through the region by early Tuesday evening, it packed a punch: Isaias's winds were recorded moving as quickly as 70 miles an hour at John F. Kennedy International Airport, Mr. de Blasio said.

At one point, 911 dispatchers received more than 100 calls a minute from New Yorkers trying to report downed trees and power lines, he added.

A 60-year-old man in Queens died Tuesday after a tree collapsed onto the vehicle he was sitting in, and a woman in Brooklyn was critically injured by a falling branch that hit her while she was walking in Brownsville, Brooklyn around 2 p.m. Tuesday, according to NYPD officials. The woman was transported to a nearby hospital where she received treatment, according to the officials, who didn't know if she had been released from the hospital as of Wednesday afternoon.

"Job one is to make sure there's no additional danger to human life and to make sure that cleanup is done safely and quickly," Mr. de Blasio said.

Workers were hauling away trees and branches that toppled onto roads, sidewalks and cars. Mr. Cuomo said crews with dump trucks, excavators, chain saws and portable generators were working throughout the state to help clear roads and clean up debris.

As of Wednesday morning, New York City had received 18,206 reports of damaged or fallen trees and limbs, according to the Department of Parks and Recreation. The department added that some of the reports were likely calls made about the same tree.

Manhattan appeared to be largely spared from tree damage, with just 570 reports logged to the parks department, while Queens and Brooklyn accounted for nearly half of the reports made across the city.

Isaias poses one of the first major tests for the parks department as it operates under a substantially tightened budget. Over the summer, the city approved a roughly $37 million cut to the department's maintenance budget, which helps fund tree maintenance and cleanup efforts.

Several commuter rails and transit services remained disrupted after the storm.

Metro-North Railroad said several of its trains in Connecticut and New York were either operating with delays or had been replaced by buses while crews worked to repair extensive power and signal outages and clear trees from tracks. The Staten Island Railway train service said it also was running with delays, while NJ Transit said service for many of its train lines would remain suspended or operate on weekend schedules.

More than 250 trees fell onto NJ Transit tracks during the storm, said New Jersey Gov. Phil Murphy.

"It will be a number of days before everyone is back on their feet," Mr. Murphy said. He urged residents who had lost power to take advantage of the state's cooling centers as the weather heats up.

Connecticut Gov. Ned Lamont declared a state of emergency Wednesday in response to the widespread power outages caused by the impact of the storm.

"With more than 700,000 customers experiencing power outages, we need to take several emergency steps that will facilitate restoration," Mr. Lamont said.

Katie Honan, Ben Chapman and Joseph De Avila contributed to this article.

Write to Akane Otani at akane.otani@wsj.com