Federal prosecutors began tying the string together on their case that former Probation commissioner John J. O’Brien and two top aides ran a rigged hiring system, getting a former chief deputy to admit that personnel decisions were made to curry favor with legislators who were in positions that allowed them to boost the budget and power of the agency.

John F. Cremens Jr., the first deputy commissioner under O’Brien until he retired in 2008, said he, O’Brien, and other agency officials would often have lunch together at the cafeteria in the state office building at 1 Ashburton Place and discuss preferred candidates for openings in the Probation Department.

“Generally, he would cut you off and say he would have to control the hiring, that he had to take care of the Legislature and other people looking for jobs,” Cremens said under questioning by Assistant US Attorney Fred Wyshak in US District Court. When Wyshak asked why O’Brien had to take care of lawmakers, Cremens said, “For the funding that we needed for programs that we wanted… We had to consider [legislators] when we were hiring.”

O’Brien and former first deputy Elizabeth Tavares, who replaced Cremens when he retired, and former deputy commissioner William Burke III, are charged with racketeering, conspiracy, bribery, and mail fraud for allegedly operating a fraudulent hiring system where the chosen candidate would get the position even if it required fudging scores to make it look like O’Brien’s preferred candidate was the best one.

Cremens, who sat in on the final interview panels for many of the candidates, said the best candidate did not always get the job. When asked by Wyshak to name candidates who were selected that were not the best, the one name he came up with was James Rush, the father of then-state Rep. Mike Rush, who is now a state senator. James Rush was appointed chief probation officer in West Roxbury District Court. He died in 2011, the subject of numerous complaints, including sexual discrimination and retaliation for complaints.

When Wyshak asked if the fact that James Rush was the father of a state representative was central in his appointment, Cremens answered, “Yes, it did.”

Cremens said promoting people based on political connections hurt morale among those in the department who wanted to advance but were passed over by cherry-picked applicants.

“Those people were very alienated that they were unable to be successful candidates for promotions,” Cremens said. “It affected me mentally. It bothered me what was going on.”

Related: Another Probation official made cash donation to Petrolati But it didn’t bother him enough to tell Judge Robert Mulligan, then the Chief Justice of Administration and Management, what was going on under his nose. Under questioning by Wyshak, Cremens said he would meet about once a month with Mulligan, who was the statutory boss of O’Brien, because the commissioner’s relationship with Mulligan had deteriorated during Mulligan’s tenure even though O’Brien supported him for the job initially. During his meetings with Mulligan, Cremens said the judge on several occasions questioned the pick for a position and would hold up an application he had on his desk and say he thought that person was a better candidate.

Cremens admitted he never told Mulligan about the hiring practices at Probation but admitted he should have. “Yes, I had an obligation [to tell him,] but I did not do it,” Cremens said.

Cremens also admitted he lied to Paul Ware, the special counsel appointed by the Supreme Judicial Court to investigate the Probation Department after the Boston Globe ran a damning series on the hiring practices of O’Brien and his ties to the Legislature. Cremens said he told Ware there was nothing amiss in an effort to protect himself and others.

“It may have been protection of people who were involved at the time in the hiring,” Cremens said. “I didn’t know where the investigation was going at the time.”

Defense attorneys took different tacks to discredit Cremens’s testimony. Tavares’s attorney, Brad Bailey, pushed Cremens to admit he had met with prosecutors and an FBI agent following his first day of testimony to go over more questions. Cremens said he learned from the FBI agent he was considered an unindicted co-conspirator, something he said surprised him even though his attorney had negotiated an immunity agreement prior to his testimony with prosecutors. Cremens also testified that Tavares was not a participant in the Ashburton lunch meetings.

Stellio Sinnis, O’Brien’s court-appointed federal defender, focused on Cremens’s $84,000 annual pension, intimating to jurors that Cremens could lose his pension if his testimony contradicted what prosecutors wanted him to say. Cremens responded that the immunity agreement allowed him to “testify freely.”

Burke’s attorney, John Amabile, highlighted Cremens’s background as the son of a former state representative and a brother of a judge, intimating he used his connections to get jobs and promotions. Amabile had Cremens read referral letters written on his behalf as well as confirmation letters that were signed by and copied to judges and lawmakers.

There was a small uproar toward the end of Cremens’s time on the stand when, under questioning by Wyshak on redirect, Cremens said he learned he was considered an unindicted co-conspirator while talking with “a couple other witnesses.” Judge William Young has ordered witnesses sequestered from one another and prohibited them from being in the courtroom before they testify. Cremens’s statement caused defense attorneys to look at each other with surprise and call for an immediate sidebar. A witness can be disqualified if they violate the sequester, but attorneys would not say afterward whether Cremens’s disqualification was brought up in the sidebar.

OTHER PROBATION NEWS

Among those taking in the testimony yesterday was J.W. Carney, the attorney who defended James “Whitey” Bulger in his recent federal trial.

Jurors continue to ask questions of witnesses through the judge at a brisk pace. Jurors write down their questions and then pass them to the court clerk, who passes them to Young, who decides whether to ask the question or not. The questions are also shown to each attorney before it is asked. Young asked four juror questions yesterday.