The Capitol Police department is facing a significant budget shortfall, prompting officials to put two civilian employees on administrative leave and scramble to rework the agency’s finances.

Senate Sergeant-at-Arms Terrance Gainer confirmed Wednesday that the department is now about $6 million short because officials neglected to account for issues such as attrition and weekend hours.

Police Chief Phillip Morse recently discovered the discrepancy, Gainer said, and has since been “assessing what the error was, how to remedy that error and … how to prevent it in the future.”

The department’s budget for fiscal 2010 was about $328 million, which included money for the equipment, overtime and salaries for almost 2,000 officers and hundreds of civilian employees. Gainer conceded that the shortfall would need to be made up somewhere else in the department’s budget, but he said officials were confident that they could find a solution.

“This is not an insignificant amount of money, but it certainly can be made up — with some hurt,” said Gainer, who is on the Capitol Police Board, which oversees the department.

Morse is scheduled to testify Thursday before the Senate Appropriations Subcommittee on the Legislative Branch to discuss the department’s fiscal 2011 budget, and Members are expected to bring up the issue. A Capitol Police statement attributes the shortfall to “administrative errors” that led to miscalculations in the original budget preparation.

Morse will make adjustments to the “general expense account” to cover the shortfall, according to the statement.

“These adjustments will not in any manner adversely affect the law enforcement, security or protective operations of the Department,” the statement reads. “Further, all established salaries and benefits of USCP employees will not be adversely affected.”

The department has already put two civilian employees on administrative leave because of the shortfall. Capitol Police officials declined to discuss the details or identify the positions of the employees, but Gainer said Morse “had in place protocols in how to instruct the budget, and it appears not all those protocols were followed.”

“The chief lost confidence in a couple of people,” he said. “We’re examining what the role was and how you deal with that.”

Upon hearing rumors of the shortfall, officers worried that the difference would be made up in their cost-of-living increases — which had yet to be approved more than two months after the beginning of the year. But Capitol Police spokeswoman Sgt. Kimberly Schneider said the department was waiting for the National Finance Center to process the raises, and on Wednesday the department announced that the raises were approved and will be retroactive to Jan. 3.

But the administrative error that led to the shortfall is still certain to disturb the Capitol Police’s oversight committees. The agency has had several problems with its administrative arm since it took over its own payroll and budget in 2003. The Government Accountability Office has made dozens of recommendations on the department’s finances and hiring practices — many of which officials have acted on — but problems still persist.

In 2008, for example, the department pushed 15 recruits to resign after it was discovered that they didn’t pass some aspect of their background, psychological or physical tests. The mishap contributed to the removal of then-Human Resources Director Jennifer McCarthy, who had been on the job only a year. Former HR Director Jan Jones stepped down in 2007, followed soon after by other top administrative officials, such as Chief Administrative Officer Tony Stamilio.