A top lawyer at the Department of Veterans Affairs got almost $126,000 in performance bonuses during a five-year period in which the agency imposed an illegal rule that drew the threat of sanctions from a federal appeals court.

John H. "Jack" Thompson, deputy general counsel at VA, received $125,945 in performance bonuses between 2007 and 2011, the most of anyone at the agency.

Thompson's regular salary was $179,700 in 2011, the most recent year available, according to a database published by the Asbury Park (N.J.) Press.

Thompson is one of a dozen top VA officials who each received merit bonuses in excess of $100,000 over the five-year period, according to a database compiled by The Washington Examiner.

Others include top administrators of veterans' health networks, some of which are under fire over patient deaths, unsanitary conditions and poor-quality care.

VA paid out almost $16.9 million in performance bonuses from 2007 through 2011.

The Washington Examiner reported Wednesday that top Veterans Benefits Administration officials both in Washington and in regional offices throughout the country reaped big bonuses, even while the waits for veterans seeking disability benefits skyrocketed.

The agency has canceled 2012 bonuses for the VBA. Other bonuses to some workers in the agency's headquarters and health care network "have been deferred pending further review and are not being paid at this time," according to an agency spokeswoman.

It is not known how deeply Thompson was involved in drafting or defending the rule that limited the duty of the Board of Veterans Appeals to assist veterans with disability claims. Thompson would not comment and referred calls to the VA's press office, which would not comment on individual bonus recipients.

But as deputy counsel, Thompson is the second in command at VA's legal department.

The rule, passed in August 2011, improperly stripped veterans of certain due process and appeal rights, an appeals court later found. It was challenged by the National Organization of Veterans' Advocates a month after it was issued.

The Department of Justice, which represented the VA in court, subsequently refused to defend the rule, and VA ultimately agreed to scrap it. VA officials repeatedly promised to fix the damage done to veterans by re-examining cases in which the rule was improperly applied.

After NOVA was able to prove the rule continued to be used illegally, the U.S. Court of Appeals for the Federal Circuit issued a blistering order in March threatening agency officials with sanctions.

The judges singled out the VA office of general counsel for criticism, saying lawyers there promised to review cases in which the rule was improperly applied, but failed to do so.

"The unwarranted denial of benefits means real-world consequences to veterans," the court concluded, giving the agency until mid-May to come up with a plan to correct its errors. "Promises of hypothetical relief do not pay for food or provide needed medical care."

David Hobson, executive director of NOVA, would not comment on Thompson or the merits of the VA's legal team, in part because the case is still pending.

"VA's handling of our case has been disappointing, and has done a disservice to the veterans it is supposed to be protecting," Hobson said.

"First, VA issued a regulation that was plainly wrong under federal law -- so wrong, in fact, that the Department of Justice refused to defend it in court.

"VA then promised NOVA and the court that it would stop applying the illegal regulation. But VA broke that promise, and it continued to rely on the regulation when denying veterans their claims for benefits," he said.

Mark Flatten is a member of The Washington Examiner's Watchdog investigative reporting team. He can be reached at mflatten@wwashingtonexaminer.com.