The FBI has done at least one interview with him, and under the cooperation agreement, he may be asked to do more interviews, the official said.
While he has turned over documents to the FBI related to his management of the Clinton server, investigators sought to interview him because they believed he could shed light on the period during which the server was set up and any discussions with Clinton and her aides about the security for a system that would be storing sensitive government information, according to the official.
Clinton has said she set up the private system for convenience, in order to avoid carrying more than one mobile device to access government and private emails.
Pagliano's attorney would not comment to CNN.
The probe into Clinton's use of a private email server while leading the State Department 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.
Wednesday night, Brian Fallon, a spokesman for Clinton's presidential campaign, told CNN that the former secretary of state "has been cooperating with the Justice Department's security inquiry, including offering in August to meet with them to assist their efforts if needed."
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."
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.
The Pagliano immunity agreement has caught the interest of Republicans on Capitol Hill. Sens. Charles Grassley of Iowa and Ron Johnson of Wisconsin, chairmen, respectively, of the Senate Judiciary and Homeland Security committees, are requesting a copy of the immunity agreement.
"The Committees believe that Mr. Pagliano possesses unique information about Secretary Clinton's private email account and server that is vital to the Committees' ongoing inquiries into this matter," the pair wrote in a letter to Attorney General Loretta Lynch.