Neurosurgeon J. William Bookwalter was examining a colleague’s patient who had back troubles when he made an unusual discovery: The operation that his colleague billed Medicare for was far more extensive than the one actually done, according to allegations contained in a lawsuit.

A review of two more back operations performed by UPMC neurosurgeon Ghassan Bejjani on another patient yielded the same result, including once when an insurer was billed twice for removal of the same back vertebrae. Another neurosurgeon who examined one of Dr. Bejjani’s patients two months later found the same billing discrepancy that Dr. Bookwalter uncovered, which resulted in higher reimbursement for UPMC for work that was not done, the lawsuit said.

“I certainly don’t review all of Dr. Bejjani’s cases, but occasionally see someone as a second opinion,” an unnamed UPMC neurosurgeon complained in a letter to UPMC Shadyside Hospital officials, a 2012 whistleblower lawsuit unsealed July 25 said. “If only a fraction of those had a post-operative myelogram to definitely show what was done intraoperatively, and within a short period of time the two people that fit this description were both overbilled for their procedures, it certainly would make one wonder.”

UPMC patients may be left wondering, too, after the Justice Department on Wednesday settled overbilling claims, with UPMC agreeing to pay $2.5 million to the Justice Department without admitting liability. The three-count whistleblower lawsuit brought by Dr. Bookwalter, retired neurologist Robert Sciabassi and UPMC Presby Hospital surgical technician Anna Mitina — all former UPMC employees — outlined a wide array of overbilling practices and a culture that the lawsuit alleges prized payments from insurers over patient safety.

UPMC officials were out of the office Thursday and unavailable.

Previously, UPMC said it conducted an internal review of the billing matter and has cooperated fully with the U.S. Attorney. But Dr. Benjjani continues to see patients at UPMC, receiving $2.2 million in salary and related compensation in 2014, the latest year available.

The civil lawsuit is continuing against UPMC, even though the U.S. Attorney’s office will no longer be involved in the case. In a statement Wednesday, UPMC said it reported billing irregularities as soon as they were discovered and would defend itself vigorously against any related claims.

Dr. Bookwalter, now on staff with Greater Pittsburgh Orthopaedic Associates, an independent physicians’ practice, did not return calls. Settling with the Justice Department on Wednesday in addition to UPMC were affiliates University of Pittsburgh Physicians Inc., UPMC Community Medicine Inc. and Tri-State Neurosurgical Associates-UPMC.

The 2012 lawsuit portrayed a neurosurgery practice at UPMC in which operations were made needlessly complex to drive up reimbursement from insurers, where lesser-trained medical professionals operated on patients unsupervised while the health system received payments for training doctors, even though supervising physicians were not always in the operating room as required.

Robert Friedlander, chair of UPMC Neurosurgery, last year described UPMC’s 32-member neurosurgical group as the “biggest in the country,” but only about a dozen of the doctors were implicated in the 2012 lawsuit. In addition, Amin Kassam, the previous head of neurosurgery who was accused of urging surgeons every month to increase the number of procedures performed, left UPMC in November 2013 for an executive position at Aurora Health Care’s St. Luke’s Medical Center in Milwaukee.

Dr. Kassam did not return calls.

A similar crisis involving accusations of physician wrongdoing at Greensburg-based Excela Health in 2011 elicited a very different response from hospital administrators. A yearlong probe found that 192 patients received heart stents unnecessarily between 2009 and 2010. The doctors who did the operations left the hospital system as Excela went public with the findings and helped affected patients see other heart doctors.

Excela hired Nashville, Tenn.-area consultants Jarrard Phillips Cate & Hancock Inc. to handle communications as CEO Robert Rogalski emphasized the importance of transparency in addressing the problem and publicly expressed “deepest apologies to these patients and their families.” Reassuring patients is key in such situations, Jarrard partner Molly Cate said, and so is effectively communicating with doctors.

“Doctors have a strong appetite for knowing what the hospital has done to address this effectively,” she said. “People trust their physicians more than anyone else, so the health system needs to tell patients it’s still safe to come there and the situation has been fixed.”

Kris B. Mamula: [email protected].