The US Secretary of State has said that cross border terrorism is hindering both Pakistan and Afghanistan and that the two nations should work in tandem to fight terrorism.

"We know that there is a cross-border fertilisation of extremism and terrorism," Clinton, who was in Afghanistan for the inauguration of President Hamid Karzai's second term, said.

"Afghanistan cannot get control over its territory and defeat the Taliban if they can go across the border into Pakistan as a safe haven," she said according to the transcript of the interview.

Likewise, Pakistan cannot eradicate the people that threaten them and the government if they can seek shelter across the border in Afghanistan, she said. "That's why we look at Afghanistan and Pakistan together when it comes to this fight against terrorism."

Having recently visited Pakistan, Clinton said she knows that the Pakistani military is working very hard in South Waziristan, and they do have to have precedence as to how they will use their resources and their troops.

"But we will continue to press them to go after all of the extremists in Pakistan, some of whom target Pakistan, some of whom, as you know, target Afghanistan. And we think there has to be an effort to root out the extremists in Pakistan who threaten Afghanistan," she said.

"So that is the message that I took to Pakistan when I was there a few weeks ago. It's the message that I continue to stress with our friends in Pakistan," Clinton said.

In another interview, Clinton said the US has a national security interest in going after the organisation of terror that Al Qaeda has assisted to unite, which includes elements of the Afghan and Pakistan Taliban.

"It is a direct threat to the US, to our allies, our interests, our values.”

"And we are determined to defeat Al Qaeda," she said.