ALTAMONT — The former chief operating officer of Peter Young Housing, Industries, and Treatment pleaded guilty on Wednesday to two counts second-degree offering a false instrument for filing, a misdemeanor.

Jacquelyn Gentile had served as the COO of the program in Altamont and the one in Troy for more than 29 years. She could face up to one year in jail for each count.

Father Peter Young, a Catholic priest, used to run 121 not-for-profit addiction treatment and rehabilitation programs; he had more than 18,000 people in treatment each day. That number has now fallen below 8,000, he said yesterday, in large part due to the nearly four-year investigation by Attorney General Eric Schneiderman.

Young was forced to close the rehab center bearing his name, in Altamont, in March 2014.

Now, Young said, people struggling with addiction are suffering because of the attorney general’s investigation.

He said that throughout his 60 years of work with drug and alcoholic addicts he has saved the state money by reducing the re-incarceration rate by making sure his clients received treatment; had clean, safe, and sober housing; and got job training.

A broad investigation began when the organization self-reported an internal theft.

In April 2014, right before he was set to testify in front of a grand jury, Young told The Enterprise he believed the error discovered in the investigation was “an administrative mistake,” a sentiment he echoed this week.

“You make mistakes,” said Young. “You don’t get to vet everything as much as you want to.”

He said, in filing reports to the government on where grant money is going and how it’s being used, if there is a mistake in any amount, it’s automatically considered a “misappropriation of funds.”

He acknowledged, though, that the mistake is a violation of the law, even if there were no ill intent.

In 2014, Young explained his own understanding of what might have happened with the grant misappropriation, referencing something called block grant funding, which is awarded to help residents of specific counties or communities.

“You can’t use the funding from one county on someone who doesn’t have that county of origin,” said Young.

The charges brought against Gentile by Schneiderman’s office say that her reports falsely claimed that grant funds in excess of $600,000 were being spent for a drug and treatment center in Brooklyn when they were actually spent on programs in upstate New York.

“Lying to a state agency in order to illegally obtain grant funding is unacceptable and will be prosecuted,” said a press release from the attorney general’s office.

Young maintains that Gentile did not lie in order to get money from the state. She simply made a mistake in reporting how funds that had already been received had been used, he said.

“We will stick with what we said in the press release,” said Deputy Press Secretary Nicholas Benson when asked to respond to Young’s explanation.

“I totally respect Jacque,” Young told The Enterprise. “She is full of integrity.

“She was there for the mission and not the money.”

Young said no one, including Jacque, benefited from the “mistake” she made. There were no personal gains to her as a result of it.

“She did not steal,” he said.

“It was a mistake and mistakes aren’t supposed to happen,” said Young. “But I have made a great contribution to the state and I wish the attorney general could see it that way.”

Assistant Attorney General Christopher Baynes of the Attorney General’s Public Integrity Bureau is prosecuting the case.