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State Police troopers who patrol Logan International Airport, the Seaport, and other Massachusetts Port Authority properties will now be paid directly by the beleaguered law enforcement agency under a newly hatched agreement spurred by officials’ failure to disclose years of payroll records for the unit.

The deal, announced Tuesday after officials from both agencies huddled in a closed-door meeting, comes on the heels of a Globe report showing that neither the State Police nor Massport had publicly filed information on payouts for Troop F with the state comptroller since 2010.

The revelation sparked blistering criticism from lawmakers and Governor Charlie Baker, who charged that the lack of disclosure was “clearly deliberate,” and it highlighted the unusual pay structure for the 140-trooper division.

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Massport, an independent public agency that owns and operates Logan, Seaport properties, and two other airports outside Boston, currently pays the troopers directly, accounting for more than $32.5 million in spending last year alone. But the troopers are State Police employees, and the troop’s operations are overseen by State Police commanders.

That will now change, according to Massachusetts comptroller Thomas Shack. The troopers will move to the State Police’s payroll, and Massport will reimburse the law enforcement agency directly. With this change, the Troop F funding arrangement mirrors that of Troop E, which patrols the Mass Pike and is funded by MassDOT.

“We’re satisfied that we have a path and a plan for correcting this issue and getting the information up and transparent as quickly as possible,” Shack said after officials from all three agencies met in his office Tuesday.

He said officials also ironed out a plan to get the missing payroll records uploaded to the comptroller’s website in the coming days.

“We had a productive meeting with the comptroller and Massport today,” said David Procopio, a State Police spokesman. “The State Police are eager to move forward with them to make sure Troop F payroll data is shared and made publicly available, going back to 2010 and for the future.”

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Massport spokeswoman Jennifer Mehigan said, “We had a productive meeting that produced a short-term fix and a long-term change.”

Shack said that after meeting with two agencies, he does not believe there was “anything nefarious” behind the lack of disclosure. Mehigan told the Globe that officials did not file records with the comptroller’s office because they considered work done by the troop’s employees to be akin to services provided by a vendor.

“It certainly wasn’t the right thing to do, but I certainly don’t get the impression that anybody, certainly in this generation of leaders, had any malicious intent to not provide transparency,” Shack said.

The disclosure of the Troop F payroll was only the latest turmoil to hit the State Police, which has 2,150 troopers and handles a range of duties, from patrolling the Mass Pike and Logan to investigating homicides.

On Friday, nine troopers were suspended without pay and nine more retired in the face of an investigation into overtime abuses. Attorney General Maura Healey’s office has also launched an investigation. The department’s handling of the arrest of a judge’s daughter — and revelations that the former colonel ordered the scrubbing of the report — has also sparked at least three separate probes.

The scrutiny into the embattled agency doesn’t end there, however.

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State Auditor Suzanne Bump has launched an audit into the State Police’s Commonwealth Fusion Center, the department’s anti-terrorism data clearinghouse, a person with knowledge of the situation told the Globe.

Michael Wessler, a Bump spokesman, would only confirm that the office is auditing the State Police, and that a review was launched as part of the office’s regular churn of statutorily mandated audits into state agencies.

But Procopio, the State Police spokesman, confirmed the center is the focus of what he called a “routine program audit.” He said the center was chosen by Bump’s office because it “has a unique critical mission in the state.”

“The audit is focusing on the operation of the CFC in its entirety, not on any specific section or function of the Center,” Procopio said. “Specifically, the audit is reviewing our systems and procedures for maintaining, sharing, and expunging data, and is not reviewing the data and contents within those systems. Therefore, no sensitive or criminal history information is being shared with the auditor.”

The Fusion Center was launched in 2005 in Maynard, where a variety of local and state public safety agencies collect and analyze information about potential terrorist threats.


Matt Stout can be reached at matt.stout@globe.com. Matt Rocheleau can be reached at matthew.rocheleau@globe. com.