This story has been updated to include a comment from the FBI on the status of improvements.

FBI special agents and technicians say the agency’s first-ever, decade-in-the-making computerized case system has slowed their investigations and work, according to an internal audit.

The computer application, called Sentinel, was flipped on in 2012 to make cases easier to search, both for clues and possible links to other ongoing investigations. Previously, FBI personnel had shared information, approved documents and updated files by circulating piles of paper.

An inspector general report released Wednesday finds the majority of employees feel the program has had an "overall positive impact on the FBI’s operations, making the FBI better able to carry out its mission, and better able to share information."

But a subset of employees, including special agents and technicians, report that headaches with the new system, such as ineffective searching and burdensome indexing, persist.

For example, most special agents reported they spent more time filling out database fields to improve search results, which "leaves less time for investigative activities,” according to the report. The process of filling in the boxes for items such as date of birth, aliases and other fields is called "indexing."

Buggy Search Engine to Blame

About 67 percent of FBI technicians, who keep records of evidence and move evidence in and out of storage rooms, said "Sentinel had a negative impact on their daily productivity," according to the report.

Indexing and searching, two of the system's major functions, irked some other employees too.

Only 42 percent of employees surveyed for the audit said they received the search results they needed. The problem largely has to do with buggy search engine filters.

"Sentinel returned either too many search results for users to reasonably review or no results at all for a document the user knew existed," IG officials said.

The evidence-custodian technicians and electronic-surveillance technicians represent a small number of FBI employees polled by the IG, but they make up a large portion of the userbase. Most spend more than 30 hours a week on the system.

Evidence-custodian technicians now must maintain two chains of custody for each piece of material, a paper version and an electronic one. The technicians type duplicate files, because Sentinel is intended to serve as a backup if the paper chain of command is ever lost or destroyed.

The FBI told inspectors that searching is being enhanced through "training, new algorithms, and other technological improvements to reduce the frequency of false positives and negatives among search results," according to the report.

In addition, Sentinel 1.5 -- the system's first upgrade, scheduled to be deployed next month -- should improve other search-related features.

On Thursday afternoon, FBI spokesman Christopher Allen said Sentinel 1.5 "will be rolled out beginning this weekend."

Price Tag Grows on Second Attempt to Digitize Case Files

This is the second attempt at a networked FBI case system. After starting development in 2001, FBI pulled the plug on the first program, called the Virtual Case File, in 2005, at a loss of $170 million.

Since going live in 2012, Sentinel's budget has crept up about $100 million, and is now is slated to cost $551 million. The increase was attributed to operations and maintenance and new functions developed during fiscal 2014.

A high-performing Sentinel, however, could actually save money in the future, auditors said.

"If Sentinel 1.5 successfully subsumes other legacy systems or improves the integration of Sentinel with other legacy systems, the FBI should realize cost savings from retiring systems and reducing the amount of maintenance to operate other legacy systems," according to the report.

In response to a draft report, bureau officials recognized the difficulties with searching and indexing and committed to addressing their employees' concerns.

"The FBI will solicit the feedback of Sentinel users to ensure search function improvements effectively reflect the user needs," Jeffrey Johnson, FBI assistant director for information technology engineering, said in a Sept. 12 letter.

In addition, bureau officials will research technological fixes and review business processes to find ways of cutting the time it takes to index large, uncategorized documents, he said.

FBI officials were not able to immediately comment on the status of improvements.