The searches in Massachusetts, New York and New Jersey were the product of evidence gathered in the investigation, but there was "no known immediate threat to the public or any active plot against the United States," FBI spokeswoman Gail Marcinkiewicz said.
Asked at a news conference for details about the three men picked up Thursday morning, Holder said "we believe" there is evidence that they were providing Shahzad with funds.
Holder said "one of the things we are going to be trying to determine" is whether the men knew they were supplying funds for an act of terrorism.
The attorney general's comments followed a day spent on Capitol Hill, where Republicans on the House Judiciary Committee initially took him to task for the Obama administration's approach to fighting terrorism - relying heavily on the criminal justice system to handle suspected terrorists.
Three people were arrested on suspected immigration violations: the two Pakistani men in the Boston area and one person in Maine, U.S. Immigration and Customs Enforcement spokesman Brian Hale said. All three arrests are administrative and not criminal, he said. The three were not immediately charged with any terrorism-related offenses.
The two Boston-area men had a "direct connection" to Shahzad, a Pakistan-born U.S. citizen, said a top Massachusetts law enforcement official. Investigators weren't sure whether they were witting accomplices or simply moving funds, as is common among people from the Middle East and Central Asia who live in the U.S., said the official, who spoke on condition of anonymity because the investigation is ongoing.
"These people might be completely innocent and not know what they were providing money for, but it's clear there's a connection," the official said.
Authorities are now trying to determine the source of any money that might have been moved to the Boston-area men.
"That's the focus of the ongoing investigation," said the official.
All three of the men arrested on suspected immigration violations are Pakistani, according to another law enforcement official. Two of the men have overstayed their visas and the third is already in removal proceedings, said the official, who was not authorized to discuss the ongoing investigation and spoke on condition of anonymity.
Police cordoned off a small house in Watertown, a suburb about 10 miles west of Boston, and a neighbor reported seeing an FBI raid there.
A Mobil gas station in Brookline, another Boston suburb, also was raided. The entrances and exits to the station were cordoned off by yellow tape, and FBI agents were going in and out of the building. Agents also searched and removing items from a silver Honda Accord in the parking lot.
The car was registered to Mohammad Zameen, 45, said Ann Dufresne, a spokesman of the Massachusetts Registry of Motor Vehicles. Zameen also is listed as a resident at the apartment in Watertown. No one answered phone calls at his listed number.
Marcinkiewicz said the arrest in Maine was part of the investigation into the Times Square bomb plot, but said she had no additional details about the arrest.
"They're all connected, but the specifics to Maine I don't specifically know what they were doing," she said.
Homes were searched in Centereach and Shirley, N.Y., both on Long Island.
"I am targeted. I am looking at it this way being a Muslim and being Pakistani," Mohammad Iqbal said.
Feeling like a target and being surprised at his front door, Iqbal says two FBI agents began questioning him in the early morning hours.
"'You mind if we search your house?' I said I have nothing to hide, go right ahead. Go search whatever you want. I have no problem at all," Iqbal explained.
With his family in fear he says they questioned him for five and half hours, showing him pictures and asking if he knew Faisal Shahzad.
Mohammed told Eyewitness News that he had only seen Shahzad in the newspapers and on television after his arrest.
"Never met him. Never hear heard his name. Never knew where he belonged from, where he lived. Even in New York. Even in Pakistan," he said.
Sources are telling Eyewitness News that Shahzad took an LIRR train to Ronkonkoma back in April where he then traveled to another location to meet with a man who sources say gave him four-thousand dollars.
Just four miles from the station, federal agents converged on another house in Center Reach during their raids on Thursday.
Agents converged on a basement apartment, which is rented, the landlord says, by Mohammed Yumus. Yumus lives here with his wife and daughter.
A woman inside on Thursday yelled through the door at reporters, "Go pick on a real terrorist. Moron."
In New Jersey, the FBI searched a home in Cherry Hill, N.J., and a print shop in Camden, N.J., said FBI spokesman J.J. Klaver in Philadelphia.
Two brothers, Muhammad Fiaez and Iqbal Hinjhara, live at the Cherry Hill condominium, Fiaez said. He said his brother owns the print shop.
Authorities arrived at their home at 6 a.m., Fiaez said, questioned him and his brother on how long they have lived in the U.S. and on the business. After questioning, the FBI told Fiaez he wasn't of interest to them.
Shahzad has been in custody at an undisclosed location since his arrest on May 3 from a Dubai-bound plane at Kennedy Airport. He has waived his right to an initial court appearance and will appear in court as soon as he is finished talking with investigators, U.S. Attorney Preet Bharara said Thursday in White Plains, N.Y. Federal investigators say he has told them he received weapons training in Pakistan.
Elias Audy, 61, of Boston, is listed at the owner of the Mobil station. He was seen by reporters leaving the business afterward and had no comment.
Shahzad, 30, is accused of trying to detonate a bomb-laden SUV in Times Square on May 1. Police said the bomb had alarm clocks connected to a can filled with fireworks apparently intended to detonate gas cans and propane tanks.
The vehicle smoldered but didn't explode. Federal agents, tracing Shahzad through the SUV's previous owner, caught him two days later on a plane bound for the United Arab Emirates as it was departing New York's Kennedy Airport.
There was no immediate comment from Pakistan on the raids Thursday.
Islamabad has said it was too early to say whether the Pakistani Taliban, which operates from the country's lawless northwest tribal region, was behind the Times Square plot although the U.S. said it found a definite link. But Pakistan promised to cooperate with the investigation and has detained at least four people with alleged connections to suspect Faisal Shahzad.
The Washington Post is reporting officials in Pakistan have arrested a suspect with connections to a known Pakistani militant group and who claims to have acted as an accomplice to Shahzad. An unnamed senior US law enforcement official would not say what "evidence" led them to the arrest.
Vinny Lacerra, 50, who lives across the street from the house raided in Watertown, said he was in his living room about 6 a.m. when he heard somebody say, "FBI! Put your hands up!" Lacerra said he looked out his windows and saw 15 to 20 FBI agents with their guns drawn surrounding the house.
About 15 minutes later, the agents went inside and came out with one man handcuffed and took him down the street, he said. He also said he saw an agent from Immigration and Customs Enforcement.
"I was surprised to see this, because this is what you see on TV," Lacerra said.
There was no indication that Audy, the gas station owner, was a target of the terror probe.
Audy was born in Lebanon, and came to the United States at 19 to study at the University of Houston in Texas and then at Northeastern University in Boston near his brother, according to the website of a used car dealership Audy also owned.
"He's very, very philanthropically-minded as a businessman, very involved in his community," said Harry Robinson, executive director of the Brookline Chamber of Commerce.
Robinson said Audy has a wife and family and has been a longtime U.S. resident. Robinson also said he was not only involved in the chamber, but the local Rotary club.
Shahzad had been living in Connecticut. William Reiner, FBI spokesman in Connecticut, there were no search warrants served in the state Thursday as part of the investigation.
Some information from ABC News and The Associated Press