Holder said there was nothing to suggest that the government of Pakistan was aware that Shahzad, 30, intended to carry out the attack.
Al Jazeera's Kamal Hyder, reporting from the Pakistani capital Islamabad, said the Pakistani government is "not at all happy with the contradictory language that is coming out of Washington".
"Just two [or] three days ago the Pakistani media was putting on its front pages this news that General [David] Petraeus had said - and they quoted him - that the alleged mastermind of the [failed] Times Square bombing was a lone wolf.
"After that statement, the US secretary of state warned Pakistan of severe consequences if a link was established and/or there was a deadly attack in the US."
Holder's comments came as the New York Times reported that the United States warned Pakistan it must crack down on Islamic extremists or face severe consequences.
John Brennan, the White House deputy national security adviser, echoed Holder's charges, pointing the finger at the Pakistani Taliban in an interview with CNN.
"It looks like he was working on behalf of the TTP, the Pakistani Taliban," Brennan said.
"This group is closely allied with al-Qaeda. This is something that we're taking very seriously."
General Stanley McChrystal, the US commander in Afghanistan, urged Pakistan's General Ashfaq Parvez Kayani in Islamabad on Friday to quickly begin a military offensive against the Pakistani Taliban and al-Qaeda in North Waziristan.
Shahzad was pulled off a plane bound for Dubai and arrested on Monday for allegedly leaving a four-wheel-drive vehicle rigged to explode in New York's Times Square just over a week ago.
Al Jazeera's Rosiland Jordan, reporting from Washington DC, said the latest disclosure was a "turnaround from a week ago when the US government believed that Faisal Shahzad was acting alone".
"But Mr Shahzad has continued to talk to the investigators, but they have not been clear about the extent of the Pakistani Taliban involvement evidence, but it is worth mentioning that Shahzad was placed under US watch list a few years ago because he came to the US at one point with $80,000.
"You have to declare anything that is over $10,000 if you are taking it in or out of the US.
"Authorities felt then that there was something that was not right about him bringing in so much cash. Up until recently he was under very low key surveillance."