ORANGEBURG — Cash-strapped South Carolina State University continues to push forward with building the James E. Clyburn University Transportation Center, despite scathing audits and losing its designation as one of the country’s federal transportation centers.

The university continues to hold aside $1.6 million from its 2012-2013 budget for construction of the next building in the troubled complex. That money would come from tuition, state appropriations and the South Carolina Education Lottery. Meanwhile, school leaders worry about how they will cover the cost of basic operation in the upcoming school year amid declining student enrollment and tuition revenue.

Eric Eaton, the school’s new associate vice president for finance, presented an updated budget Tuesday to the university’s Board of Trustees. It includes $1.6 million for the Emily E. Clyburn Archives, which is the second building in the first phase of the planned transportation complex.

That money would go toward the required $3 million in “matching funds,” school officials have said. The university has $24 million in federal money available for the first phase of the transportation center, but it needs to provide some money from private, state or other sources before it can access most of the federal funding.

The transportation center came under fire in 2010 after The Post and Courier reported that more than $50 million had flowed to the center — about half for a new building and half for transportation research and education programs — but the site for the new building was vacant, no transportation research was under way, and it had lost its federal designation.

A subsequent investigation from the state’s Legislative Audit Council, which was released in June 2011, cited severe management problems, and estimated that the transportation complex likely would cost about $107 million. The university had no viable plan for raising the rest.

An audit on about $391,000 from the state Department of Transportation, which was released in the spring, found additional financial irregularities, and concluded that S.C. State should be designated a “high risk grantee.”

Eaton told the board that even though the money for the transportation center is in the budget, it might not be spent because he doesn’t expect construction to begin on the new building during the current fiscal year, which runs through June 30.

He did not elaborate on the reasons why construction likely would not begin.

Board member Maurice Washington asked that the budget be changed and the $1.6 million for the transporation center be used instead for academic services for students. “The quicker we come to a decision that we can’t afford it, the quicker the president can come up with a budget we can rally around,” Washington said.

Board member Anthony Grant said a budget is a fluid document. If school leaders later in the year find that they can’t afford to spend the money on the new building, they can put off construction.

John Corbitt, the board’s acting chairman, said that made sense, The school is dealing with many financial issues, he said, and $1.6 million is not a large amount in comparison. “We’ve got some big, big problems,” Corbitt said, “and $1.6 million is the least of it.”

Board members did not come to a decision on the matter but will continue discussing budget issues at an Aug. 28 Finance Committee meeting.

Eaton said declining student enrollment is a large factor in S.C. State’s budget uncertainty and financial woes.

The current version of the budget is based on an enrollment of 4,180 students. School leaders don’t expect to meet that target number, Eaton said.

University spokeswoman Erica Taylor said after the meeting that the school could not release enrollment numbers until after students arrive on Aug. 20. She could not yet predict how short enrollment might fall.

Eaton also said the university continues to carry a deficit from previous years, and that it couldn’t make up that shortfall in just one year.

Taylor said she could not yet estimate that deficit because school employees still are in the process of closing out the 2011-2012 fiscal year.

Reach Diane Knich at 937-5491 or on Twitter @dianeknich.