Colorado’s Department of Corrections is wasting as much as $44 million annually because it has not fixed problems in a treatment program intended to prepare sex offenders for release from prison, a recent state audit found.

An analysis by auditors showed that nearly 1,300 prisoners in December 2015 had passed their parole eligibility date but had not received sex-offender treatment. It determined the potential cost to taxpayers by calculating the annual cost for their prolonged incarceration.

Delays in treatment are especially problematic for lifetime-supervision offenders, who must complete the treatment before they can be released from prison, according to the audit. Problems in the department’s Sex Offender Treatment and Monitoring program effectively keep these offenders in prison indefinitely. Others, who face fixed sentences, are released without treatment that is supposed to reduce recidivism, according to the audit.

“When the Department does not effectively allocate its limited resources and does not establish and maintain a working system to prioritize and enroll the sex offenders most in need of treatment while incarcerated, it creates significant public safety risks, inequities, negative financial impacts, and negative impacts on treatment effectiveness,” the performance audit from state auditor Dianne Ray’s office said.

While conceding many of the audit’s findings, corrections officials say that most of those who have not completed the treatment either did not want to enroll or failed to complete the program. The audit was released in November but provoked blistering criticism from legislators during a joint Judiciary Committee hearing this week.

Auditors also found that prison doctors were failing to enter mental illness information into the department’s computer system. Three prisoners with severe mental illnesses ended up in solitary confinement in 2014 and 2015, even though state law bars putting the mentally ill in such restrictive settings.

Prison officials say doctors now are entering the mental health information correctly into the computer system. They added that a new $22 million computer system, the first phase of which is being installed this month, will allow them to ensure such information is being correctly recorded in the future. In addition, officials now review paper records in prisoner files before putting a prisoner in solitary confinement.

“There are such massive inefficiencies in this, and we’re struggling with a budget crunch,” said Rep. Joe Salazar, a Democrat from Thornton during a hearing Wednesday that reviewed goals and priorities for several state agencies. “This is a $44 million problem. What are you doing to address the inefficiencies?”

Corrections officials said they are struggling to fix the sex-offender treatment program, which was the subject of a critical audit in 2013. They said problems are exacerbated by a shortage in treatment providers and difficulties in tailoring the program so it is not spending too much time treating lower-level offenders.

“The problem is in getting people who are specialists who can do this work,” said Kellie Wasko, the deputy executive director or corrections. “We have shortages and vacancies, but it’s not like there are a large number of people out there with the proper certification to be a sex offender clinician.”

The legislature increased funding from just over $2.5 million annually to about $4 million annually in the last three years to hire 15 more clinicians for the sex offender program, but the corrections department has not been able to increase staffing and has struggled with staff turnover, according to a state report from the legislature’s budget-writing Joint Budget Committee.

Enrollment in sex offender treatment has plunged as the department struggled to find clinicians. In 2012, there were 92 new sex offender enrollments in the sex offender program, but the new enrollments had decreased to 68 by 2015, and have continued to decline, according to the committee report.

Because of an inability to find sex offender clinicians, corrections officials this year want to redirect about $1 million in annual appropriations for the treatment program toward paying for other needs. Instead, they want to steer the money toward hiring more teachers at Sterling Correctional Facility and for increased departmentwide maintenance, according to the Joint Budget Committee report.

“It’s our obligation if we need it for something else and we can hire or fill for that, then we need to do that,” Wasko said in an interview Thursday.

She said the department also hopes to reduce a current backlog of nearly 1,700 prisoners on the sex offender treatment referral list by making changes that would mean lower-level sex offenders receive less rigorous treatment than they currently do.

The corrections department already has made changes to the program in hopes of lessening the amount of time lower-level offenders spend in treatment, Wasko said. The department plans to seek approval to make more extensive revisions to the program that should allow lower-level offenders to complete it sooner, freeing up more capacity.

Wasko said many of those on the referral list either have refused to undergo treatment or have been kicked out of treatment for failing to adhere to the program, which requires an admission of guilt. As of Thursday, 67 lifetime supervision offenders who are beyond their parole eligibility date have requested treatment and been unable to enroll. Of those with fixed sentences beyond their parole eligibility date, 369 who have requested treatment remain on the waiting list, she said.

An 18-year-old law created the lifetime-supervision sentence for Colorado sex offenders. The law established indeterminate sentences — two years to life, for example — for many sex crimes in Colorado. Sex offenders who successfully complete a prison-treatment program and get paroled then enter a community-based lifetime-supervision program.

By 2016, more than 2,414 offenders in Colorado prisons were sentenced under the law, or nearly 9 percent of the prison population, according to legislative staff reports.