Revelations about an alleged overtime scam, a wave of suspensions, and hefty pay for Massachusetts State Police troopers have sparked scrutiny of the state’s largest law enforcement agency.

But troopers’ actual earnings are much higher than previously reported, and new disclosures raise further questions about the agency’s spending, oversight, and transparency.

Payroll records for an entire 140-trooper State Police division — including some of the department’s highest earners — have been hidden from public view and weren’t filed with the state comptroller for several years, the Globe has found.

The records for Troop F, which polices Logan International Airport and parts of the Seaport, among other areas, accounted for more than $32.5 million in spending last year and portray a lucrative, overtime-laden operation that outpaces the compensation totals of troopers working in other State Police divisions.

For example, Thomas J. Coffey was paid $351,774 last year, including $137,091 in overtime pay, making him the second-highest earner in the agency, behind only the former superintendent.

Neil R. Calnan collected $309,315, including $157,282 in overtime pay, working for Troop F.

At least 79 percent of Troop F made more last year than Governor Charlie Baker, who earned $151,800. The percentage would be even higher if you included the pay that some workers received in 2017 for time spent in other State Police divisions.

Fourteen Troop F members earned more in overtime than in base pay, including Michael S. Fiore, who collected $164,607 for overtime and $134,133 in base pay.

“The State Police should be concerned that some of its members are making such extraordinary amounts of money on overtime work,” said David Tuerck, a Suffolk University economics professor and president of the Beacon Hill Institute, a conservative research center. “There should be a limit on the amount of overtime pay a State Police officer can have.”

The records for Troop F, which polices Logan International Airport and parts of the Seaport, among other areas, accounted for more than $32.5 million in spending last year John Tlumacki/Globe Staff

The records also show that 393 troopers normally assigned to other State Police divisions worked detail and fill-in shifts for Troop F, collecting another $6.4 million.

In the entire department, at least 299 troopers — about 14 percent — made more than $200,000 last year. Fifty-four of them were assigned to Troop F, a division that’s highly sought after by the department’s 2,150 troopers.

State officials acknowledged the number of highly paid troopers is even greater than detailed in this story. With some troopers appearing on two payroll lists, the number is impossible to tally due to incomplete data that officials provided to the Globe.

Troop F is paid by the Massachusetts Port Authority, an independent public agency that owns and operates Logan, Seaport properties, and two other airports outside Boston. But the troopers are State Police employees, and the troop’s operations are overseen by State Police commanders.

When the Globe raised questions last week, the State Police and Massport had not filed Troop F payroll records with the state comptroller’s office since 2010. The comptroller oversees and publishes state finance data.

“We were unaware that the data was missing until you brought it to our attention,” Comptroller Thomas Shack said in an e-mail.

Shack said both agencies should be transparent with the trooper payroll.

“Even if they are assigned to Massport, they are still ‘state’ troopers,” he said in an e-mail. “We will work with the State Police and Massport to get that data in the system as soon as we can.”

For several years, the State Police have publicly released payroll statistics without Troop F. The agency repeatedly claimed that the pay for all of its employees was listed on the comptroller’s website.

In addition, the State Police have repeatedly refused to release troop assignments.

Secretary of State William Galvin’s office, which handles public-records appeals, ordered the State Police to provide the troop locations of its workers in January, but the State Police refused to comply and have asked Galvin to reconsider.

Massport for years had released pay data for all personnel, save for Troop F, and said that all of its payroll was available through the comptroller. The agency released the Troop F pay to the Globe late last week.

Massport spokeswoman Jennifer Mehigan said officials there did not file records with the comptroller’s office previously because they considered work done by Troop F employees to be akin to services provided by a vendor. She said Massport is working to provide records dating back to 2010 to the comptroller.

Mehigan noted that nearly all of the agency’s operational costs are paid with money it generates from its various properties, including fees from airlines and people parking in lots it owns.

State Police spokesman David Procopio referred questions to Massport.

Elizabeth Guyton, spokeswoman for Governor Baker, said he “believes Massport should have publicly posted detailed payroll information from the onset” several years ago and that Baker “agrees with their decision to post information with the comptroller’s office for all employees now.”

Five of Massport’s seven governing board seats are controlled by Baker.

The payroll issues come amid a series of State Police scandals that have chipped away at public confidence.

Some legislators have hinted that they would hold oversight hearings in light of the scandals.

On Tuesday, Colonel Kerry A. Gilpin revealed that 20 active troopers and one retiree face sanctions in an overtime abuse scandal in Troop E. The troopers allegedly logged hours they did not work, with some alleged violators putting in for as many as 100 no-show shifts.

On Friday, State Police said nine of those troopers were suspended without pay, nine more retired, and one was kept on active duty.

Another trooper, prior to Tuesday’s announcement, was already suspended without pay and under investigation in another matter.

Attorney General Maura Healey’s office is reviewing Troop E’s alleged overtime abuses for potential prosecution.

Employees in Troop E, which patrols the Massachusetts Turnpike, are ultimately paid by the Department of Transportation under an arrangement that’s similar to the one State Police have with Massport for Troop F.

However, Department of Transportation spokesman Patrick Marvin said that MassDOT “does not employ any Massachusetts State Police troopers, meaning no officers are paid through MassDOT’s payroll.”

Instead the department reimburses State Police for the troopers’ services. Troop E records have been included in previous payroll disclosures.

For years, troopers have fought Boston police to maintain their exclusive right to have Troop F patrol Massport property along the South Boston Waterfront. More jurisdiction means higher staffing levels, overtime, and detail pay.

There has also been infighting within the State Police, with unionized troopers arguing that higher-ranked nonunion workers should not be assigned to work overtime shifts.

In 2014, Lieutenant Warren Yee filed a lawsuit against the State Police, claiming the department discriminated against him in not transferring him to Troop F, “a desirable assignment, because it offered the opportunity to earn considerably more compensation than other posts.”

In another case in 2007, a trooper took legal action to secure an assignment to Troop F.

Massport officials said seniority is a key factor in who is assigned to Troop F and that results in troopers with more vacation time, and thus more overtime is necessary.

Mary Z. Connaughton, director of government transparency at the Pioneer Institute, a nonprofit think tank that supports limited government, said the latest overtime disclosures merit more examination.

“You don’t need to be Nostradamus to predict that the overtime corruption at the Mass. State Police is not isolated to a single troop,” she said. “The lack of transparency leads the public to cast further doubt on the agency.”

She suggested that the historically secretive agency publicly post detailed timesheets each week.