The next victim of the United States debt crisis could be conditional loan guarantees, says a prominent venture capitalist.

The loan guarantees are one of the financial engines powering many cleantech investments in Silicon Valley.

“I think the loan guarantee programs could go away,” Kleiner Perkins Caulfield & Byers partner Ray Lane told VentureBeat. “I think everybody is concerned about the loan guarantee program, fewer are concerned about (the Advanced Technology Vehicles Manufacturing Loan Program) ATVM.”

A loan guarantee from the Department of Energy helps companies attract buyers and investors for new renewable energy projects. It means the government will foot the bill if the project does not take off or is unable to produce some kind of return for investors. It’s one of the ways the U.S. government is promoting renewable energy.

The loan program comes in three flavors: the 1703, 1705 and ATVM programs. The ATVM program is specifically designed for electric car manufacturers. That program probably won’t go anywhere because of rising gas prices and because of a desire to make the United States as “clean” as other countries with very high gas prices.

The U.S. government has allotted an enormous amount of money to companies like solar panel manufacturer First Solar. The program has issued conditional guarantees valued at around $16 billion to solar power projects and $38 billion to clean technology projects. Other countries stimulate cleantech expansion by other means, like feed-in tariffs. While the loan program is important, Lane said it might not be the right way to approach cleantech funding.

“The role of the government isn’t necessarily to give out loans but to stimulate innovation, and I think we are dangerously close to the government getting out of that role,” he said. “If you look at the amount of greentech R&D this country did over the past couple of years, it’s really tiny; we basically had a $1 billion R&D budget.”

One of the U.S. Department of Energy’s most stellar programs is the Advanced Research Projects Association – Energy, he said. That program allots between $3 million and $5 million for highly disruptive clean technology projects and will likely endure the debt crisis because it is popular, low-cost and has a high potential to create innovative technology, he said.