Justice Department officials have said that Abdulmutallab decided to stop speaking with federal investigators the day after the attempted bombing, even before he was given a Miranda warning by FBI agents.
During questioning from Sen. Olympia Snowe, R-Maine, Mueller became agitated over the politicization of the case.
"I encourage you to look at what has happened since then," he said. "And it is a continuum in which, over a period of time, we have been successful in obtaining intelligence not just on day one, but day two, day three, day four, day five and down the road. And so I encourage you to look at it as a continuum as opposed to looking at is as a snapshot of what happened on one day."
Sources tell ABC News that FBI agents went to Nigeria and identified influential members of Abdulmuttallab's family who disagreed with what he did, and then brought them back to the United States to talk with him.
At Tuesday's hearing Blair said of the case, "The balance structure in the Mutallab case was understandable and balanced. We got good intelligence. We're getting more."
According to Justice Department and counterterrorism officials, the accused Al Qaeda in the Arabian Peninsula operative has provided some details about his handlers in Yemen and others who were training with him.
The discussions between Abdulmutallab, his lawyers and federal investigators began last week as Justice Department officials explored the possibility of offering Abdulmutallab a plea deal in exchange for his cooperation and information he has about the terror network.
A Justice Department spokesman declined to comment on the plea discussions, and Abdulmutallab's attorney Miriam Siefer did not reply to an email message.
Sen. Kit Bond, the ranking Republican on the Intelligence Committee told Blair he disagreed with the conclusion that the case was handled properly because the suspect has been giving investigators information.
"There should be a decision made after consultation with the relevant agencies and the intelligence community when an enemy combatant comes in, before the Department of Justice gives the order to Mirandize him," the Missouri Republican said. "He's an enemy combatant and the decision ought to be made by the intelligence -- with the participation of the intelligence community."
The decision to issue a Miranda warning to Abdulmutallab was reached by the FBI's chief of counterterrorism in conjunction with Justice Department attorneys, Mueller said.
Since the attempt to bring down flight 253, both Republicans and Democrats have questioned how the Justice Department handled the case, but Feinstein today said decisions should be made on a case-by-case basis.
"Candidly, my view is that the president should have the flexibility to make a determination based on the individual circumstances of the case -- the location of the terrorist activity, the location of the arrest, the nationality of the suspect, whether federal crimes or law of armed conflict have been violated," Feinstein said.
ABC News' Pierre Thomas contributed to this report.