A project to modernize the University of Washington’s payroll system is costing millions more and taking longer than expected.

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A new system to manage pay and benefits for the University of Washington’s 44,000 employees is six months behind schedule and costing millions more in consultant fees than expected.

But the project is expected to stay within its budget because the UW is delaying some technology improvements to save money, said Kelli Trosvig, vice president for information technology and chief information officer for the UW.

Trosvig said that when the project to revamp the UW’s payroll system began last year, the UW didn’t assign enough employees to work through the many complex issues, leading to the delay. The university also had to make changes to the original contract, she said.

The contract is with Workday, a publicly traded California software vendor. Its clients include Hewlett-Packard, Yahoo and Amgen, as well as Carnegie Mellon University, Georgetown University and Lewis & Clark College.

The university’s homegrown payroll system is more than 30 years old and relies on the programming language COBOL. The system manages payroll for two hospital systems — UW Medicine and Harborview — as well as the UW’s three campuses. It’s made doubly complex because many employees are in unions, with different contracts and benefits.

The initial contract with Workday was for $27 million. Trosvig said the UW now expects it will need to pay Workday an additional $3.3 million, covering the cost of six months of extra work.

The UW Board of Regents budgeted $67.5 million for the project this past year — a number that includes the salaries of UW staffers needed to implement the program. Of that budgeted amount, $10 million was earmarked as contingency, to pay for cost overruns. It’s not yet clear how much of that contingency will be needed to finish the project, she said.

The UW had to make a major change to the contract when administrators realized they couldn’t set up the system to pay employees biweekly — that doesn’t line up with the way the Washington state system issues pay and benefits, Trosvig said. Instead, paychecks will continue to be issued twice a month, which means two fewer paychecks over the course of a year.

She said the university will save money by delaying a planned streamlining of the undergraduate admissions-application process, the conversion of the entire UW work force to a uniform email and calendar system, an upgrade of the UW’s telephone service, and an emergency data backup system, among other projects.

When it goes live, the pay and benefits system will automate many types of record-keeping jobs for the university, and the UW will have “much better data about how our dollars are spent,” she said. Audits and compliance reports, too, will be built into the system. “It will be quite an amazing difference,” she said.