Thorp said he did not think enrollment at UNC Chapel Hill would be affected.
The announcement means massive layoffs could be coming to many of UNC's 16 campuses across the state.
In a message to the entire university system Wednesday, President Erskine Bowles said: "We're gonna lose hundreds of people. It's gonna have a real effect on the University."
Bowles said 400-500 people will be let go. He also said class sizes will grow, faculty-student ratios will worsen, and security personnel will be trimmed.
In a memo to UNC employees, Thorp called the cuts "painful." He said as the Legislature begins to debate the budget, it was in the best interest of the university not to delay making tough choices.
"We're hopeful that cuts to the UNC system ultimately will be minimized. But even so, we already know that what we at Carolina do - and how we do it - will be significantly affected," he said. "The longer we wait to enact inevitable cuts, the deeper the cuts likely would be."
Thorp said he did not foresee the cuts leading to the layoffs of tenured faculty members or the cancelling of fixed term contracts.
He also said the university would do what it can for workers who lose their jobs.
"Last month, I authorized Brenda Malone, associate vice chancellor for human resources, to create the Employee Assistance Fund to enhance the outplacement services we provide for people who have been laid off. We expect those services to be in place soon," he said.
Thorp also said he supports the idea of furloughs for workers to help the budget crunch and urged the Legislature to act on that idea, but he said even a quick decision wouldn't be sufficient to cover the entire university system's budget shortfall.