He returned from Pakistan in February and told authorities he spent five months there visiting his parents, according to the criminal complaint filed in US District Court in New York.
Earlier on Tuesday, five men were reported to have been arrested by security officials in Pakistan in connection with the attempted bombing.
"Intelligence officials arrested two in the city of Karachi in the southern city of Punjab and three more in Faisalabad," Kamal Hyder, Al Jazeera's correspondent in Pakistan, said.
"Shahzad's father-in-law was also one of those arrested," Hyder said.
"His parents house has been located in Peshawar but apparently the parents left once they heard about their son's arrest," he said.
Our correspondent said that according to witnesses in the neighbourhood, Shahzad had been there a few months ago to attend a wedding.
"It would be interesting to see if there are any links between all these arrests and whether they will be able to get any clues."
The department of justice said that Shahzad was arrested when he tried to board a flight from New York's John F Kennedy airport headed to Dubai, in the United Arab Emirates.
"The FBI's quick action was critical as he was arrested in JFK as he attempted to flee," Holder said.
"We also coordinated with everyone to ensure the arrests of everyone that is responsible for this."
Barack Obama, the US president, said that the FBI and other authorities are investigating the suspect for possible connection to terrorist groups.
"They have all the tools and experience they need to learn everything we can and that includes what, if any connection, this individual has to terrorist groups," Obama said during a live statement from Washington DC on Tuesday.
He said that the attack was a sobering reminder of current security threats, but vowed that "as Americans and as a nation we will not be terrorised."
Our correspondent said that reports from Pakistan confirmed that Shahzad had an ID card issued from Karachi and his family lived in a middle class neighbourhood.
"What is important is that around the same time the attack was discovered, the Taliban in Pakistan immediately took responsibility and a video tape with open threats was released within 24 hours," Hyder said from Peshawar.
Rehman Malik, Pakistan's interior minister, said that they will co-operate with American officials in their investigation.
John Terret, Al Jazeera's correspondent in New York, said that custom officials had recognised Shahzad from pictures which must have been circulated to US authorities and not released to the media.
"There is some doubt [as] to whether Faisal Shahzad was arrested on the plane or whether the plane was pulled back as it was started to get ready for take off," Terret said.
Kimberly Mertz, an FBI agent, said that a home believed to be Shahzad's, in Bridgeport, Connecticut, was searched earlier on Tuesday.
"He's claimed to have acted alone, but these are things that have to be investigated," an official said.
"Faisal was born in Pakistan and was naturalised as an American citizen less than a year ago," Terret said.
Dubai-based Emirates confirmed on Tuesday that flight EK202, scheduled to leave New York for Dubai at 11pm local time Monday night, was called back by authorities shortly before taking off.
"Three passengers were removed from the flight," a spokesperson for the airline said.
EK202 was the only flight scheduled to leave New York for Dubai on Monday night, implying that Shahzad was one of the passengers removed. Emirates wouldn't disclose the identities of the other two passengers.
US media reported earlier, quoting law-enforcement sources, that the suspect was a Connecticut resident and apparently paid cash for the vehicle found in Times Square.
The four-wheel-drive vehicle, a Nissan Pathfinder, was rigged with a crude propane-and-petrol bomb.
The registered owner of the vehicle had told police on Monday that he had sold it three weeks ago without any paperwork to a man in his late 20s or early 30s.