The Massachusetts Department of Transportation failed to audit tens of millions of dollars in funding it sent to Massachusetts State Police, even as overtime programs it paid for became centerpoints of a fraud scandal that has led to investigations of 40 troopers.

Under state law, MassDOT is responsible for paying for all state police operations on the Massachusetts Turnpike and metropolitan highway system.

The agency signed a memorandum of understanding with state police in 2010 agreeing to fund Troop E, the now-defunct division previously responsible for patrolling the Mass. Pike and Boston tunnels. The agreement gave MassDOT the authority to audit any reimbursements sought by state police.

On Wednesday -- hours after federal authorities announced the first charges issued against troopers accused of abusing MassDOT-funded overtime programs -- the agency confirmed to MassLive that it had never exercised that power.

The disclosure comes nearly two months after MassLive first requested copies of any existing audits, and following multiple administrative appeals and threats of litigation over the agency's violations of public records law deadlines.

MassDOT told MassLive it is now working to strengthen financial controls and will begin regularly auditing transactions with state police.

Asked to comment on the agency's handling of the funding, the office of Gov. Charlie Baker pointed to state police reforms announced in April, including a commitment to conduct quarterly audits of top earners that will be publicly released.

"The Baker-Polito Administration and Colonel [Kerry] Gilpin are implementing several new reforms at the State Police, including the elimination of Troop E and strengthening auditing procedures, to restore the public's trust and improve accountability within the Department," Baker's Deputy Communications Director Sarah Finlaw wrote in a statement.

The alleged overtime abuse, which has already led to the dissolution of Troop E and federal charges against three troopers, centered on two overtime programs: Accident Injury Reduction Effort (AIRE) patrols, which were four-hour overtime shifts designed to reduce crashes on the Mass. Pike, and X-Team patrols targeted aggressive driving.

MassDOT funded the patrols to the tune of about $1 million per year, according to figures provided by state police. Those payments ended in 2017, when the programs were suspended after a state police internal audit identified suspicious overtime claims by Troop E trooper Eric Chin.

The investigation against Chin launched a full audit of the program, which in turn led to a series of suspensions and retirements, a federal grand jury, the implementation of GPS tracking on state police cruisers and the three criminal cases announced Wednesday against troopers Gary Herman, 45, of Chester; Paul Cesan, 50, of Southwick; and Lt. David Wilson, 57, of Charlton.

But state police funding documents obtained through a public records request show that until Chin's behavior raised red flags, the use of the abused programs was expanding. State police requested $1.46 million in funding for AIRE and aggressive driver overtime in fiscal 2017 -- a $350,000 increase over the previous year.

State and federal authorities are scrutinizing Troop E overtime payments from 2015, 2016 and 2017, Gilpin has said. But through each of those years MassDOT filled reimbursement requests without auditing how the money was spent, the agency said Wednesday.

The agency noted in its response to MassLive's questions that it was not required to audit the reimbursements under its funding agreement with state police.

It is unclear exactly how much was allegedly stolen. The troopers arraigned Wednesday are accused of stealing a total of about $50,000, by a combination of skipping shifts and cutting out early. The troopers allegedly substantiated their overtime claims by filing false citations, known in the troop as "ghost tickets."

But those troopers were just three of the approximately 40 whose use of overtime is under investigation, and U.S. Attorney Andrew Lelling said Wednesday that the charges were "the beginning and not the end" of the federal investigation.

MassLive first requested copies of any existing audits on May 4. The agency failed to respond with the 10-day legal deadline for public records requests. MassLive appealed to the state Supervisor of Records office, who ordered the agency twice to respond immediately.

MassDOT again did not send a formal response, prompting MassLive to retain Boston-based attorney David Lurie, who sent the agency a demand letter on June 21 warning of a potential lawsuit if they did not comply with the order. MassDOT confirmed there were no audits six days later.