"These are not the same features that are costing us more, but we are adding additional features," said Mayor Ara Najarian.
About 150 employees in the city's community planning and fire departments use the system for tasks, including all building and safety permitting, code enforcement and annual Fire Department inspections of local businesses.
City officials in 2007 recommended buying the new interface to replace the city's current system, which they said was outdated and not able to support remote Internet access.
The system was slated to be completed early last year, but it has been delayed repeatedly as officials try to migrate to the new program.
The portion of the system used by the Building & Safety Division went live last month.
"We underestimated the poor quality of the data that was in the old system," said Information Services Director Ed Fraga, who joined the department in June 2009. "When we brought it over, it just didn't work."
Despite the delays and added costs, city officials say EdgeSoft's system is still the best available option.
"This is still less expensive than the alternatives that we looked at way back then," Fraga said. "We bought this with the expectation that there would be additions to it."