Pentagon officials have issued dire warnings in recent days about the potential impact of the cuts. The cuts will be compounded by the fact that the department did not receive an appropriation for this year and is being funded by a “continuing resolution” that keeps spending at 2012 levels.

Officials say 2012 funding levels are about the same as 2013, but the budget priorities are different and much of the money is in the wrong accounts. The Pentagon, they say, has little flexibility to shift funds between accounts and is facing a significant shortfall in some areas.

Kendall said talks with industry would help both sides prepare more effectively.

“Engaging in this dialogue will allow industry to more productively make their own internal business plans to deal with potential sequestration impacts,” Kendall said in the memo.

“Feedback from industry will provide valuable insights as government managers decide how best to move forward in attempting to meet the war-fighter requirements and DoD (Department of Defense) needs under severely constrained budgetary conditions.”

Kendall’s memorandum also encouraged program managers and grant officers to quickly notify companies and universities carrying out Pentagon research about any plans to reduce their grants or awards funding.

“Program and awarding officials ... should work together to notify recipients as soon as practicable after decisions about reductions are made so that recipients have as much time as possible to adjust their program execution plans,” Kendall’s memo said.

The acquisitions chief said communication would need to be more limited if proprietary information were involved or if the contract was in the process of being awarded.

“However, as a general rule, transparency with industry and academia while we plan for potential sequestration and CR (continuing resolution) is in the department’s long-term best interests,” Kendall said.