Almost as quickly as it came, the smell of gas left Manhattan and parts of New Jersey yesterday, leaving authorities no closer to determining where it came from.

Before the odor dissipated, several New York City agencies and the United States Coast Guard launched investigations and some train service was temporarily suspended. A number of buildings in Midtown turned off their HVAC systems to keep fresh air out, while others were evacuated, officials said.

Through the Web site of the city’s Office of Emergency Management, authorities assured the public that the odor was not harmful. But the city still stank.

“It was a real foul odor,” a man who works at 1350 Broadway near Herald Square, Gary Sandler, said. “I was actually getting a headache from it and a little nauseous.”

A shopkeeper on West 34th Street also noticed the smell. “Outside, I couldn’t really breathe,” M. Pervez, 57, who declined to give his full first name, said.

At a news conference around 11 a.m., Mayor Bloomberg said he was confident the odor was not dangerous. He said the city’s air sensors did not detect elevated levels of natural gas, which is odorless, and speculated that an additive to natural gas, mercaptan, could be to blame.

The mayor discounted a small gas leak that was reported on Bleecker Street in Greenwich Village as too small to cause the pervasive odor. “It may just be an unpleasant smell,” he said.

Officials said hundreds of 911 calls began coming in around 9 a.m., when the smell was at its worst. Reports came from across the city, from Rockefeller Center to Battery Park, officials said.

At 9:10 a.m., PATH trains from Journal Square and Hoboken in New Jersey to 33rd Street in Manhattan were suspended as a precaution, a Port Authority spokesman said. Service was restored shortly after 10:30 a.m., he said. The 23rd Street station on the subway’s F line also was closed between 9:47 a.m. and 10:11 a.m., according to a spokesman for the Metropolitan Transit Authority.

On West 34th Street, sirens blared as fire trucks responded to gas-related calls. By 2 p.m., 12 people complaining of dizziness and difficulty breathing had been taken to area hospitals, a spokesman for the Fire Department said.

In a city full of smells, some people expressed concern about the city’s safety.

“I wondered if something was going to explode,” a woman who works in Midtown, Diane Liewehr, said. “It does cross your mind: Is this some sort of terrorism thing?”

While officials discounted any threat to New York’s safety, they could not pinpoint the source of the odor as the day wore on.

A spokeswoman for Con Edison, D. Joy Faber, said multiple crews had been out in the field since the morning, and they found no abnormal changes in gas transmission lines that would indicate a leak in the system. “We have found no gas leaks on our system whatsoever,” she said.

The city’s Department of Environmental Protection also had a mobile lab in the field late yesterday afternoon, as well as Hazmat and air monitoring crews taking samples from around the city.

“It’s still a mystery,” a DEP spokesman, Charles Sturcken, said.