A Petaluma man who served as financial director for a San Rafael-based nonprofit that provides services to local senior citizens was arrested this week on suspicion of embezzling more than $58,000 from the organization.

Steven John Thompson, 53, had already left Whistlestop when his interim replacement discovered discrepancies in the agency's books that led to Thompson's arrest on Wednesday, the nonprofit's chief executive, Joe O'Hehir, said Friday.

He said that a forensic audit turned over to police on Tuesday indicated that bank deposits made on behalf of the agency were smaller than was reflected in the accounting ledger. It appeared that when checks and cash were collected for deposit, sometimes only the checks were actually deposited, he said.

O'Hehir said Thompson was hired in January 2011 as director of finance and administration of the agency, which operates on a $6.5 million annual budget providing rides, nutrition programs like meals on wheels, classes, activities and other services to some 5,000 seniors every year. Thompson ended his employment in April of this year. O'Hehir declined to say whether Thompson left of his own accord.

The suspected embezzlement occurred intermittently from September 2011 to March 2013, and appears primarily to have involved revenues generated through the agency's public restaurant, the Jackson Cafe, though there were other sources. "The checks were deposited, but the cash was missing," he said.

O'Hehir said an interim director brought in in May found discrepancies in the books and hired a forensic auditor on advice from San Rafael Police.

The resulting audit was submitted on the eve of Thompson's arrest in Petaluma on four suspected offenses, including embezzlement, forgery, burglary and grand theft, according to Marin County Jail booking records.

Thompson posted bond for $10,000 before he could even be assigned a cell, jail personnel said, and it was unclear when he would make his first court appearance.

O'Hehir said Whistlestop's losses will be recovered through insurance and said it "does not have an impact on our clients or our services."

But he said the nonprofit's leadership was reviewing practices and controls.

The suspected theft "was a disappointing discovery," he said. "We are just handling it the best we can to make sure it doesn't happen again."

Attempts to reach Thompson were unsuccessful Friday and law enforcement agencies involved in the arrest did not return phone calls.

You can reach Staff Writer Mary Callahan at 521-5249 or mary.callahan@pressdemocrat.com.