The committee on oversight said, in a letter to John T. McDonald III, the current president of the pharmacy: “Two days after that final audit was issued, Barbara J. McDonald, your mother and president of Marra’s Pharmacy, wrote Governor Cuomo in an attempt to have him intervene in your dispute with O.M.I.G.”

“After your mother’s letter to Gov. Cuomo,” the letter continued, “O.M.I.G. further reduced the findings of Medicaid overpayments.” The agency eventually settled for $268,000.

Mr. McDonald, formerly the mayor of Cohoes and now a Democratic state assemblyman, said Friday he was happy to cooperate and provide the voluminous file showing why his family had fought the audit, eventually suing the state, and why the amount had been reduced. “We’ll be even happier when they review it and realize there was nothing wrong,” he said.

Far from receiving favoritism, he said, his small pharmacy was almost destroyed by an unforgiving government bureaucracy and is now being swept into a politicized inquiry. Medicaid requires prescriptions to be kept for six years so the government can verify that its payments are justified, but his mother mistakenly believed they could be destroyed after five, and did so. The audit sample showed 30 prescriptions missing. Auditors estimated the pharmacy had been improperly reimbursed by Medicaid by at least $1.4 million, an extrapolation technique used by James Sheehan, then the Medicaid inspector, that providers protested.

“My mother is 78,” Mr. McDonald said. “She’s devoted her life to the pharmacy.”

A second letter from the committee went to John Navarra, owner of Town Total Nutrition Inc. in Manhattan, which had been overpaid through Medicaid by more than $10 million, according to a 2007 preliminary audit. After it was disputed, the inspector general repeatedly reduced the recovery demand, eventually settling for $521,291, less than 5 percent of the initial finding.