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Several State Police supervisors regularly ordered rank-and-file troopers in a scandal-ridden unit to skip overtime shifts that they were paid for, a former trooper says in a newly unsealed court filing.

The filing, submitted by the attorneys for one of the dozens of troopers implicated in the scandal, for the first time alleges that troopers were directed by their bosses when they racked up thousands of dollars in overtime for work that they did not perform.

Commanding officers, in some cases, told troopers to “run silent, run deep” and “take a slow ride home,” according to the filing.

The widespread fraud scandal has resulted in convictions of seven troopers and drawn scrutiny over dozens more. Three higher-ranking officers have also been indicted. However, several other supervisors of the implicated troopers have avoided charges so far.

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The information was made public Friday after the Globe asked a federal judge to remove redactions that had been made to a court filing in the criminal case of former trooper Daren DeJong.

Submitted in the spring by DeJong’s attorney, the filing disclosed how DeJong had spoken with investigators at the Massachusetts attorney general’s office, telling them about how he, fellow troopers, and shift commanders for years coordinated to skip shifts and cover it up.

That section of the filing was initially sealed entirely, and until Friday, portions remained shielded from public view, concealing descriptions of how commanding officers holding the rank of lieutenant not only participated in the scheme, but directed troopers to skip some or all of their overtime shifts.

“The information DeJong provided should now help enable the Commonwealth [to] more fully connect the dots and root out those who may have had a greater understanding of the scope of corruption than the lower-level troopers who benefitted from following their orders,” said one previously redacted line in the filing by DeJong’s lawyer, R. Bradford Bailey.

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Bailey declined to comment.

Judge Mark Wolf previously said the redactions were of references to “at least four people” who have not been criminally charged. The filing did not name the individuals but merely said their rank.

State Police spokesman David Procopio declined to comment. “The department does not comment on ongoing legal proceedings,” he said in an e-mail.

In explaining his decision to lift the redactions, Wolf said he “expects that it will be necessary” to discuss the previously redacted material the next time DeJong’s case returns to court. No date has been set.

At a hearing in May, Wolf, fueled by the details of that filing, said the overtime scandal appeared to amount to “a conspiracy” and he grilled federal prosecutors about why they hadn’t pursued the type of charges often used against mobsters who engage in elaborate criminal schemes.

Including DeJong, 46 current and former sworn members of the State Police have been accused by the department of collecting overtime for hours they didn’t work, prompting the agency to disband an entire troop.

Seven troopers have pleaded guilty to federal criminal charges, and three lieutenants continue to fight charges they face at the state level. One of the three lieutenants has pleaded guilty to federal charges.

Federal and state investigations have revealed troopers were writing bogus traffic citations to meet unconstitutional ticket quotas, falsified other paperwork, and destroyed documents. Meanwhile, department officials have destroyed and lost track of records that could have exposed further wrongdoing.

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Another former trooper, Heath P. McAuliffe, who was charged and sentenced to a year of supervised release, wrote in a court filing in May that he “felt it was unfair” that almost every member of his troop used the same scheme with the knowledge of their superior officers, but “only a handful of us were singled out for federal prosecution.”

State and federal prosecutors declined to comment, citing how they are continuing their separate investigations.

Over the summer, a Suffolk County grand jury began receiving materials and testimony about an investigation into overtime fraud by another member of the department, according to a recent court filing. That case has not yet resulted in any charges.

And in late June federal authorities awarded a $17,500 contract to an outside vendor to scan and make electronic copies of about 25,000 State Police traffic tickets, which have served as key pieces of evidence in the overtime fraud investigations.

State Police have faced an unrelenting series of scandals over the past two years, prompting promises from Governor Charlie Baker and others to reform the agency. Last week, the head of the agency, Colonel Kerry Gilpin, announced plans to step down this month.

Matt Rocheleau can be reached at matthew.rocheleau @globe.com. Follow him on Twitter @mrochele .