"This company should not have been operating," United States Secretary of Transportation Ray LaHood told ABC News. "We take responsibility for bus safety and we need to do better."
Sky Express is part of a growing sub-industry of inexpensive buses on the East Coast that offer cheap fares, free wireless Internet and convenient routes.
The increasing popularity of the buses, and the rise of fatal accidents in which they are involved, have also prompted Members of Congress to call for tighter regulations.
"How many deaths do we have to have before the bus companies are going to start saying, 'Maybe we don't need more time. Maybe we should start doing something about this,' without the government telling them to," said Sen. Sherrod Brown, D-Ohio. "Sometimes they need government mandates."
Seven hundred fifty million passengers board 3,200 buses every year in the U.S. and Canada, according to the American Bus Association.
Peter Pantuso, the association's president and chief executive officer, said at the time of the Sky Express crash that there should be bigger consequences for these companies.
"We're glad to see that they were put out of service," he said. "What we would really like to see is, if this company has the safety record we're looking at, companies like this should be completely shut down."
In New York, State Transportation Commissioner Joan McDonald told ABC News affiliate WABC-7 there have been about 3,000 surprise bus inspections throughout the state since the March 12 bus crash that killed 15 people. During that period, 304 drivers and 238 buses have been taken off the road. The state does 160,000 bus inspections every year.
"There are thousands of bus operators out there, but that's not an excuse," Robert Sumwalt, an NTSB board member, told ABC News in June. "The traveling public deserves, each and every time they get on a bus, they're entitled to and they deserve a level of safety. And currently that's not always happening in all cases."
Under law, companies have 46 days to appeal the decision to put a carrier out of service and show why they should not be shut down. That can be extended by 10 days if the Dept. of Transportation needs more time to go through the evidence to decide whether to order them to close up for good.
Sky Express was given an unsatisfactory rating on April 12 and was given the 45-day period to appeal the Department of Transportation's decision. The company submitted an appeal on May 11, and was initially denied.
However, the Transportation Department then found drug, alcohol and hours-of-service concerns with the company, and extended its review period 10 days past the May 28 deadline for an official decision.
Because of the crash, LaHood decided to end the appeals process altogether and immediately put Sky Express out of service.
"There is no excuse for delay when a bus operator should be put out of service for safety's sake," he said in a statement. "On my watch, there will never be another extension granted to a carrier we believe is unsafe."
Pantuso said that there should be more inspections done on a regular basis.
"They had this long history of violations through 2009," he said of Sky Express. "Why weren't they put out of service?"
ABC News' Lisa Stark, Maggy Patrick and the Associated Press contributed to this story.