The second in command at the Massachusetts State Police retired Tuesday, and the superintendent moved up his own retirement, in the latest fallout from a growing controversy into the handling of an arrest report about the daughter of a judge.

Deputy Superintendent Francis Hughes put in his retirement papers and Superintendent Richard McKeon, who was scheduled to retire next week, moved up his retirement date to Tuesday, according to documents obtained by the Globe.

Lieutenant Colonel Dermot Quinn is in command of the State Police temporarily, said David Procopio, spokesman for the State Police, who also confirmed that both men retired Tuesday.

Procopio on Tuesday said Hughes retired because a new superintendent would want to choose his own deputy.

The union that represents troopers contends that McKeon and Hughes departed suddenly to avoid an Internal Affairs investigation.

Dana Pullman, president of the State Police Association of Massachusetts, said, under the department’s rules and regulations, a State Police trooper or official cannot retire if there is an investigation underway. The union filed a request for an Internal Affairs investigation into the arrest report on Monday.

McKeon had drawn widespread criticism for ordering Trooper Ryan Sceviour to alter the report he wrote after arresting Alli Bibaud in Worcester on charges of drunken driving and driving under the influence of drugs on Oct. 16. Her father, Timothy Bibaud, is the first justice of Dudley District Court and presides over the drug court there.

In its request for an internal investigation, the union alleged that the State Police command staff, including McKeon, Hughes, and others, “engaged in a conspiracy to violate the law by tampering with official court documents.’’

McKeon, who announced his retirement last week amid mounting criticism, had acknowledged ordering Sceviour to alter his police report to remove embarrassing comments made by Bibaud.

“We keep being told nobody did anything wrong and now the second in command at the State Police has abruptly retired,’’ said Lenny Kesten, who has filed federal suits on behalf of Sceviour and a second trooper, Ali Rei, who alleges she was also ordered to change her report.

“I think his actions speak for themselves,’’ Kesten said.

Sceviour was issued a reprimand for including the comments in his report, as was the sergeant who signed off on the report, Jason Conant.

Hughes had not been named by Sceviour or his superiors as having been involved in ordering the trooper to change his report. But when the Globe asked who decided that Sceviour and Conant should get reprimands, Procopio, the police spokesman, said the command staff made the decision jointly.

Procopio on Tuesday said the Hughes retirement would allow the new superintendent to name his own deputy.

“Traditionally, when a Colonel/Superintendent of the Massachusetts State Police leaves his or her position, the Deputy Superintendent resigns as well to allow a new Colonel to select a second-in-command of his or her own choosing,’’ Procopio said in a statement Tuesday evening. “As such, Deputy Superintendent Francis Hughes today retired from the State Police after a 31-year career.’’

In his lawsuit, Sceviour alleged he was reprimanded and forced to falsify official records to protect the judge’s daughter. He said he was ordered to remove Bibaud’s admission that she has traded sex for heroin as well as her rant that her father was a judge who would be furious about her arrest.

McKeon suggested that he was trying to treat a victim of opioid addiction with sensitivity and respect. He also said he has told troopers “more times than I can remember’’ to focus their reports only on the charges against the individual.

“In our law enforcement role, our first duty is to enforce the law and protect the public, but that doesn’t preclude us from being empathetic toward those in need,’’ he wrote in a separate resignation letter to Public Safety Secretary Daniel Bennett.

Hughes had served nearly 20 years in the Gang Unit and several years as a deputy commander in the Division of Investigative Services. He is a past recipient of the Trooper George L. Hanna Medal of Honor for Bravery and the Trooper of the Year Award, Procopio said.

Globe correspondent Martha Schick contributed to this report. Andrea Estes can be reached at estes@globe.com.