Pakistan has signalled its readiness to deal with terrorists operating within its borders as well as with those who cross over to Afghanistan, US Defence Secretary Leon Panetta said on Tuesday.

The statement followed a clarification by officials of the Defence and State Departments of a Pentagon report that tended to create an impression that Pakistan was still allowing terrorist safe havens in Fata to operate.

The officials said the report was old and since then Pakistan had carried out several “complementary operations” with Afghan and Nato forces against the terrorists.

“We are more encouraged with the fact that they want to take steps to try to limit the terrorist threat within their own country and obviously the threat that goes across the border” to Afghanistan, Mr Panetta told reporters travelling with him to Kuwait.

He said that army chief Gen Ashfaq Parvez Kayani had “indicated a willingness to try to put more pressure on safe havens”.

While “actions have to speak louder than words, I do believe they’re in a better place because they understand the kind of threats they should deal with,” Mr Panetta added.

A Pentagon report, released to the media on Monday but sent to Congress three months ago, had alleged that terrorist safe havens in Fata were preventing US and allied forces from dealing a “decisive defeat” to militants inside Afghanistan.

“The Taliban-led insurgency and its al Qaeda affiliates still operate from sanctuaries in Pakistan,” the report claimed. “The insurgency’s safe havens in Pakistan, the limited institutional capacity of the Afghan government and endemic corruption remain the greatest risks to long-term stability and sustainable security in Afghanistan.”

The Pakistan Embassy in Washington drew the Pentagon’s attention to the report, widely publicised by the media, pointing out that it did not reflect the improvements that have occurred since July this year.

In July, the United States had apologised to Pakistan over an air raid that killed 24 Pakistani soldiers last year and Islamabad reopened the supply routes to Afghanistan it had closed after the attack.

Since then the two countries have taken a number of steps to improve ties and this month they held a series of working group meetings to restart the US-Pakistan strategic dialogue after more than a year.

Secretary Panetta also acknowledged that Pakistan was helping Afghanistan in talking to the Taliban for seeking a peaceful solution to the Afghan conflict.

But reconciliation with the Taliban, he said, was not easy because of the number of factions involved in the conflict. “We have to at least make the effort to develop some kind of political solution as well as the military effort we are engaged in.”

At the Pentagon, two senior Defence and State Department officialsbriefed the media on the report sent to Congress, explaining that relations with Pakistan had improved considerably since the reporting period.

The report was apparently prepared before July, when the two countries took several significant steps to improve ties.

“We’re very encouraged by the dialogue that’s taking place between Afghanistan and Pakistan. And an important and essential part of that dialogue is the cross-border situation,” said a senior State Department official.

“So we hope that dialogue will continue. We hope and expect to see confidence-building measures from both the Afghans, and the Pakistanis.”

The United States wants to encourage that dialogue is in the interest of peace and stability “to the extent that can be helpful”, he said.

“Cooperation with Pakistan has improved during this reporting period. Pakistan agreed to reopen the ground lines of communication, which were closed in November of last year,” observed a senior Defence Department official.

Meetings with Pakistan, both bilaterally between Isaf forces, and Pakistani military forces, and trilaterally with Afghan military forces, were also going well, he added.

The official noted that Nato forces were now conducting “a growing number of complementary operations” with Pakistan, which in the last reporting had virtually ceased.

At the same time, I don’t want to leave you with the impression that we think everything is working well, because the safe havens do continue to exist,” the official warned.