Auditors from the UK, South Africa and the Philippines reported that despite spending $8.7m (£5.8m) over the past three years, the Integrated System Project is yet to go live.
Their report called on the UNHCR to strengthen project management on the scheme. The system was designed to replace an existing financial management system and support the UNHCR's service delivery.
The project involves establishing extensive enterprise resource planning and electronic document management systems.
"In its initial appraisal of the Integrated System Project, UNHCR had not quantified and ranked the likely benefits to accrue from the new system," the report said, nor had it identified the extent of modifications needed for the software to meet the high commissioner's needs.
Auditors also found that the UNHCR has yet to set up a reliable system for establishing accurate information on the refugee population.