(Adds comments on aid in paragraphs 8-9)

By Kristin Roberts

WASHINGTON, Nov 14 (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."

"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 does not want to "punish" Pakistan for Musharraf's declaration of emergency rule.

SUPPLY LINES

Morrell said the Pentagon had no indication that any U.S. funding to the Pakistani military had been diverted by Musharraf's government to implement the emergency rule. He said aid programs included checks and balances to ensure against such a diversion of funds.

"We have no indication that any of our aid to Pakistan is being used for anything but its intended purpose," Morrell said.

The U.S. military has 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 United States 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."

(Editing by David Wiessler and Bill Trott)

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