Karen Guidotti, San Mateo County chief deputy district attorney, said her office has been investigating the matter since it was brought to its attention in early December. She would not elaborate on the details of the investigation.
Mr. Hanretty's resignation was effective Tuesday, Jan. 31. Assistant superintendent Carol Piraino was named acting superintendent.
Attempts to reach Mr. Hanretty were unsuccessful.
Woodside district Superintendent Beth Polito said the district first discovered the irregularities last October. The questionable accounting dated back to a building modernization project that was completed in the 2007-08 school year, she said.
In a written statement, Ms. Polito said that, after the discovery, the district "immediately contacted legal counsel and through counsel, hired independent forensic auditors." The information gleaned from that audit led to the district's contacting the district attorney's office.
The Woodside School District, she said, "has retained independent accountants to further investigate these irregularities. We do not believe there will be any immediate negative impact on the ... district's budget."
Portola Valley school district officials have "absolutely no indication that any fiscal wrongdoing has taken place during Mr. Hanretty's tenure at this district," according to a letter from the district's school board president, Scott Parker.
"Nevertheless, in an abundance of caution, the board is working closely with the Office of the County Superintendent of Schools to retain an independent auditor to evaluate our district's finances. The district is not able to provide any further comment or details until the completion of the investigation."
Mr. Hanretty worked many years for both the Portola Valley and the Woodside elementary school districts, first as business manager, then as assistant superintendent.
He was appointed superintendent of the Portola Valley district in 2010, replacing Anne Campbell when she moved on to serve as San Mateo County superintendent of schools.
Ms. Campbell concurred that there's no indication of fiscal irregularities in the Portola Valley district, but her office is nonetheless overseeing the audit of certain areas of the district's finances. "We want to be absolutely, positively sure that everything is OK," she said. "We owe that to the public."