The cost of the City of Toronto's long-term disability benefit claims has gone up by 50 per cent over the past five years, an increase that a deputy mayor says is "really troubling."

The city covers the entire cost of long-term disability payments, which are currently being claimed by 1,285 workers.

That costs the city $42.8 million, up from $28.4 million five years ago, according to a new report by the city's auditor general.

Auditor General Beverly Romeo-Beehler is recommending more than a dozen ways to manage the program better.

Earlier this year, the city conducted a two-phase audit of its management of LTD benefits.

"The goal of the audit is to help ensure the benefit fund is administered with due diligence, and that the city LTD benefit program is integrated with best practices in early intervention, claims assessment and monitoring, as well as accommodating employees to return to work," Romeo-Beehler said in her report.​

The auditor general says one out of every 20 city employees is off work on long-term leave.

Coun. Denzil Minnan-Wong told CBC News that the increase in costs "is really troubling.

"We have to understand why and how we can get that amount down," he said.

"The Auditor General has raised significant concerns that require some serious investigation and correction to the program."

In her report, the auditor general recommends the director of the city's Pension, Payroll and Employee Benefits Division "take steps to minimize overpayments to employees receiving long-term disability benefits.

Romeo-Beehler also wants the director of the human resources division to "develop and track performance indicators for assessing and continuously improving the city's return to work process for employees in receipt of long-term disability benefits."

The city's audit committee will discuss the report at a meeting on Oct. 23 before council votes on the report's recommendations on Nov. 3.