WASHINGTON (Reuters) - The Pentagon on Wednesday said it was not worried about the security of Pakistan’s nuclear weapons amid the political crisis there, rolling back from comments made by a senior U.S. general who called the issue a “primary concern.”

An army Chinook helicopter carries military supplies as it arrives in a temporary military base in Baluchi pass in Uruzgan province, November 2, 2007. The U.S. military is looking at alternate routes to send supplies to troops in Afghanistan in case the political crisis in Pakistan makes current supply lines unavailable, the Pentagon said on Wednesday. REUTERS/Goran Tomasevic

“At this point, we have no concerns,” said Pentagon press secretary Geoff Morrell. “We believe that they are under the appropriate control.”

Last week, Lt. Gen. Carter Ham, director of operations for the U.S. Joint Chiefs of Staff, said the military was concerned about the security of Pakistan’s nuclear arsenal after President Pervez Musharraf imposed emergency rule and arrested thousands.

“Any time there is a nation that has nuclear weapons that has experienced a situation such as Pakistan is at present, that is a primary concern,” Ham said.

But U.S. defense and military officials have since backpedaled, saying the weapons are controlled by Pakistan’s military and that the military is a responsible steward of the arsenal.

Pakistan carried out its first nuclear test in 1998 and experts estimate it has material for as many as 90 weapons.

Washington considers Pakistan an important ally in the U.S.-declared war on terrorism. The U.S. military in particular works closely with Pakistani forces, especially along the Afghan border.

While the United States is reviewing all aid to Pakistan, which has received about $10 billion in U.S. funding since 2001, the Pentagon has been careful to say the Defense Department did not want to “punish” Pakistan for Musharraf’s declaration of emergency rule.

Still, Morrell said the U.S. military had begun looking at alternate routes to send supplies to its troops in Afghanistan in case the political crisis in Pakistan makes current supply lines unavailable.

The U.S. military sends 75 percent of its supplies for the Afghanistan war through or over Pakistan, including 40 percent of the fuel sent to troops, the Defense Department said.

“There are efforts under way right now to figure out contingency supply lines to our troops in Afghanistan if it becomes necessary to alter the way we now support our troops in Afghanistan,” Morrell said.

“In light of the fact that there is civil unrest in Pakistan, in light of the fact that there is a state of emergency in Pakistan, we feel it is responsible, given the importance of the Pakistani supply lines to our operations in Afghanistan, to have a contingency plan.”