The Pentagon will terminate some science and technology efforts in the coming months and cut hundreds of research grants to universities if “sequestration” budget cuts prevail, a senior Pentagon official said.

Appearing before the Senate Armed Services Emerging Threats and Capabilities subcommittee, Acting Assistant Secretary of Defense for Research and Engineering Alan Shaffer said sequestration, which started March 1, will have a notable impact on defense research, development, test, and evaluation funding. If Congress and the White House cannot reach a deal to replace sequestration with another deficit-cutting plan, defense spending will be slashed by $41 billion in fiscal year 2013, from March 1 through Sept. 30. The cuts could total $500 billion over a decade.

Sequestration is designed to cut a set percentage of roughly 9 percent across defense program elements and projects.

“So you can take whatever was appropriated in FY ’13, subtract 9 percent from that,” Shaffer said April 18 about his RDT&E portfolio. “That will cause terminations in some cases. It will cause certainly slowdowns to all of our programs.”

Shaffer said sequestration is prohibiting him from starting any new technology demonstrations in FY ’13. Where the cuts will hurt the most, he said, is in the reduction of grants and awards.

“We will reduce our overall number of grants going out to universities by somewhere between 500 and 1,000,” he said. “That doesn’t sound like much. But when we in the United States are struggling to have enough scientists and engineers to work on national-security problems, I don’t know which of those 500 or 1,000 grants might give me a very good scientist or engineer to come work in my laboratory. But if we reduce the pool, we reduce the future.”

Shaffer told Sen. Deb Fischer (R-Neb.), ranking member of the Emerging Threats and Capabilities subcommittee, that it is difficult to know which research programs to prioritize.

“We have some members in uniform who say, ‘You know, do the basic research projects that are going to pan out,’” he said. “We wish we were that good. You have to fund a number of things, and then some of them will bubble up.”

Shaffer said he has been talking with other officials in the Pentagon about how during the last two big contractions in defense spending–both under former Defense Secretary William Perry in the 1990s–research and development programs were shielded.

Perry “made a strategic choice to maintain investment in research and development, because we are cheaper and we provide options,” Shaffer said. He added he is “working through that argument” now at the Pentagon, as leaders try to determine how to manage the sequestration cuts.