Senate appropriators expressed concern Thursday over the Capitol Police’s $5.5 million budget shortfall, calling it a “disturbing” situation in a line of administrative foibles within the department.

“Your department seems to be plagued with some financial problems,” said Sen. Ben Nelson (D-Neb.), chairman of the Senate Appropriations Subcommittee on the Legislative Branch.

Capitol Police Chief Phillip Morse told Members that he discovered the funding shortfall within the department’s salaries account in his recent first-quarter budget review. Officials, he said, are still investigating the incident but believe it was the result of a miscalculation of issues such as holiday pay, loan repayments and attrition rates.

“When things don’t go right in the police department, I take full responsibility,” Morse told the subcommittee in his opening testimony. “I want to pledge to you that this type of incident will never happen again.”

Morse said he would be able to make up for the loss by taking money from the department’s general expense account, perhaps delaying projects or the purchase of nonessential items. Senate Sergeant-at-Arms Terrance Gainer — who preceded Morse as Capitol Police chief — said after the hearing that though the situation was “pretty avoidable,” he also struggled at handling the department’s administrative side.

In fact, the department’s administrative troubles have been ongoing since it took responsibility for its payroll and finances in 2003. The Government Accountability Office has written several critical reports, and in some cases, officials stepped down.

So far, Morse has put two civilian employees on administrative leave for the budget shortfall, though he emphasized that the move was standard procedure for an investigation.

Nelson and ranking member Lisa Murkowski (R-Alaska) seemed content with Morse’s explanations and spent only a small portion of the hearing — which was scheduled to discuss fiscal 2011 budget requests — on the issue.

“I think we’re going to wait until the investigation is complete,” Nelson said after the hearing. “I was relieved to hear the chief was on top of it.”