If not corrected, the shaking would arise from the powerful first stage of the Ares I rocket, which will lift the Orion crew capsule into orbit.
NASA officials hope to have a plan for fixing the design as early as March, and they do not expect it to delay the goal of returning astronauts to the moon by 2020.
"I hope no one was so ill-informed as to believe that we would be able to develop a system to replace the shuttle without facing any challenges in doing so," NASA administrator Michael Griffin said in a statement to The Associated Press. "NASA has an excellent track record of resolving technical challenges. We're confident we'll solve this one as well."
Professor Jorge Arenas of the Institute of Acoustics in Valdivia, Chile, acknowledged that the problem was serious but said: "NASA has developed one of the safest and risk-controlled space programs in engineering history."
The space agency has been working on a plan to return to the moon, at a cost of more than $100 billion, since 2005. It involves two different rockets: Ares I, which would carry the astronauts into space, and an unmanned heavy-lift cargo ship, Ares V.
The concern isn't the shaking on the first stage, but how it affects everything that sits on top: the Orion crew capsule, instrument unit, and a booster.
That first stage is composed of five segments derived from the solid rocket boosters that NASA uses to launch the shuttle and would be built by ATK Launch Systems of Brigham City, Utah.
The shaking problem, which is common to solid rocket boosters, involves pulses of added acceleration caused by gas vortices in the rocket similar to the wake that develops behind a fast-moving boat, said Arenas, who has researched vibration and space-launch issues.