updated 11/14/2007 8:59:43 PM ET 2007-11-15T01:59:43

The military is making backup plans in case the unrest in Pakistan begins to affect the flow of supplies to American troops fighting in Afghanistan, the Defense Department said Wednesday.

Pentagon press secretary Geoff Morrell said the supply lines are “very real areas of concern” because about 75 percent of the supplies, including 40 percent of vehicle fuel supplies, either go through or over Pakistan.

“We hope it doesn’t come to this,” Morrell told reporters. “Right now we’ve seen no indications that any of our supply lines have been impacted.”

The United States has about 25,000 troops in Afghanistan. Some of their supplies arrive by air from Manas air base in Kyrgyzstan. A former supply line from Uzbekistan was shut down in 2005 when the Uzbek government retaliated against Washington for what it viewed as interference in its internal affairs.

Morrell said the U.S. wanted to ensure there was a backup plan should Pakistan’s political turmoil start to affect the supply lines. “Clearly we do not like the situation we find ourselves in right now,” he said.

He did not say what potential alternative routes were under consideration and noted that some people have raised questions about safeguarding Pakistan’s nuclear weapons.

“I can tell you, at this point, we have no concerns,” Morrell said. “We believe that they are under the appropriate control.” Later he said Pakistan’s nuclear weapons are a general concern but at this stage there is no worry that the weapons are not under sufficient government control.

Last week the director of operations for the Joint Chiefs of Staff, Lt. Gen. Carter Ham, offered a different assessment of the level of concern, while not commenting specifically on safeguards.

“Certainly any time there is a nation that has nuclear weapons that is experiencing a situation such as Pakistan is at present, that is of primary concern,” Ham told reporters. “However, we’ll watch that quite closely, and I think that’s probably all I’d say about that at this point.”

No indication that funding will change
Morrell, discussing military supply lines in Pakistan, said he did not know how long it would take to switch to alternate routes. But he added, “If we needed to have it done tomorrow, we would have it done tomorrow.”

Morrell also said that there is no indication, at this point, that any of the U.S. military funding going to Pakistan is being used to enforce the state of emergency or for any purpose other than what was intended.

He said that in order to be reimbursed for counterterrorism expenses, Pakistan must submit proper documentation proving the funding is warranted.

Pakistan’s president, Gen. Pervez Musharraf, declared a state of emergency in early November and suspended the country’s constitution. In explaining his actions, Musharraf claimed the Supreme Court had meddled in politics and that terrorists posed a serious threat.

Since then the U.S. has urged Musharraf to restore democratic rule, rescind the emergency declaration and hold elections.

On Wednesday, Musharraf said he expects to step down as army chief by the end of November and begin a new presidential term as a civilian. He also warned that Pakistan risked chaos if he gave into opposition demands that he resign.

Deputy Secretary of State John Negroponte, now on a four-nation West Africa tour, will go to Pakistan on Friday to underscore U.S. concerns about the situation.

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