The FBI has been asking for Pagliano's cooperation for months as dozens of investigators pored over thousands of Clinton emails in a secure room on the fourth floor of FBI headquarters.
The probe shifted into a new phase recently as investigators completed the review of the emails, working with intelligence agencies and the State Department to determine whether they were classified.
"As we have said since last summer, Secretary Clinton has been cooperating with the Justice Department's security inquiry, including offering in August to meet with them to assist their efforts if needed," said Brian Fallon, a spokesman for Clinton's presidential campaign.
Fallon added that the campaign was "pleased" Pagliano was cooperating with the Justice Department.
Last fall, when Pagliano invoked his Fifth Amendment rights
and declined to talk to congressional investigators, Fallon said: "(Clinton has) encouraged everyone to cooperate because we want to make every good-faith effort to be transparent and answer any questions people have. With Mr. Pagliano, we encouraged him as well because we don't think he has any reason to not be transparent about the help that he provided from an IT perspective, but unfortunately, it is his choice what to do."
A message left with Pagliano's attorney was not immediately returned.
With the completion of the email review, FBI investigators are expected to shift their focus on whether the highly sensitive government information, including top secret and other classified matters, found on Clinton's private email server constitutes a crime.
The emails released publicly show some Clinton aides sent the sensitive information, often from the State Department's unclassified email system, to others, and eventually to Clinton at her private email address. She didn't use a State Department email account.
The released emails appear to align with her public statements that she didn't send emails that were marked as classified.
She did receive emails from aides that, while not marked as classified, did contain information that should not have been handled outside the government's secure email system, the emails released so far have found.
The FBI reviewers oversaw the process that upgraded the emails now known to be highly sensitive as part of a series of State Department Freedom of Information Act releases that ended Monday.
Clinton has said she hasn't been asked to be interviewed for the FBI probe.
Republican candidates quickly pounced on the development Wednesday night.
"This is an ominous development for the Clinton campaign and for Democrats as a whole," Texas Sen. Ted Cruz
told Fox News' Megyn Kelly. "This suggests that the investigation is moving to a whole other level. She is going to be a badly wounded candidate, and if we nominate a strong Republican nominee, we're going to win this general election."