"I do not know exactly what (President Pervez) Musharraf sees or thinks he sees to cause him to do what he has done," Thompson said on NBC News' "Meet the Press." Musharraf said he acted to save the country from militants.
"But we need to understand that this is a nuclear country," Thompson said. "We could face a real nightmare scenario by seeing these radical elements, or these terrorist sympathizers, take control of that government and have that nuclear capability there on the border of Afghanistan."
Thompson said the United States can not make a mistake in dealing with Musharraf.
"I think our job right now is to make sure that we know all that he knows and the reasons why he's doing what he's doing," Thompson said.
The Tennessee Republican also said the United States should "stay the course" in Iraq, and as president he would allow coercive interrogation techniques of terror suspects when lives are at stake, let colleges decide whether students could carry concealed weapons and let the states decide on abortion, though he would not favor federal funding for abortions.