In his first visit to Islamabad in three years and first under US President Barack Obama, Gates tried to reassure a public and leadership sceptical of Washington's plan to tackle militancy and turn around the war in Afghanistan.

Pakistan has seen security drastically deteriorate since joining in Washington's "war on terror" in 2001 and balks at complaints from US officials that it is not doing enough to tackle militant groups.

US drone strikes targeting Islamist fighters in Pakistan also stir anger in the Muslim nation, while many Pakistanis voice bitterness over US abandonment of the region once the Soviet Union withdrew from Afghanistan in 1989.

"I was in government in the early 1990s, when Russia left the region and the United States largely abandoned Afghanistan and cut off defence ties with Pakistan -- a grave strategic mistake driven by some well-intentioned but short-sighted US legislative and policy decisions," said Gates.

Speaking at the National Defense University in Islamabad, he said a US ban on military contacts in the 1990s over Pakistan's nuclear programme undermined a bond between the armed forces and created a "trust deficit" that lingered.

He vowed the United States was "prepared to invest whatever time and energy it takes to forge and sustain a genuine, lasting partnership" with Pakistan.

Rebuilding relationships with a generation of Pakistani officers who have had little contact with the US military will take years, Gates said.

After his speech, Gates took questions from the audience of senior military officers in a session that was closed to the media.

The "very candid" exchange included a pointed question that suggested the US-led war in Afghanistan was to blame for Pakistan's problem with violent extremists on its western border, Gates's press secretary Geoff Morrell told reporters.

The thrust of the question was "we're in this mess because of you -- to which he took great exception," Morrell said.

Gates told the officers that Afghanistan had been unstable long before the US military moved in and that it was unrealistic to assume Pakistan could be spared from the growing strength of Islamist militants.

But Gates appeared to have already rattled Pakistan's military on this trip, with comments Thursday warning that Taliban sanctuaries must be tackled or Pakistan and Afghanistan would suffer "more lethal and more brazen" attacks.

In a commentary in the English-language daily The News, Gates wrote that making distinctions between the different extremist groups -- as Pakistan is often accused of doing -- was "counterproductive".

While Pakistan has launched multiple assaults on Taliban strongholds in recent months, Washington is also anxious for Islamabad to target the Afghan Taliban and Al-Qaeda-linked militants within its borders.

Pakistan's military spokesman Major General Athar Abbas rejected Gates's description and said it was not so "black and white".

Gates also said he would ask Pakistani leaders about plans to expand its campaign to North Waziristan, a bastion of Al-Qaeda and the Haqqani network, known for attacking US and NATO troops fighting the Taliban in Afghanistan.

But Abbas told reporters no new operations would be launched until the current push into South Waziristan was complete, which would take "between six months to a year."

Gates held talks Thursday with Pakistani army chief General Ashfaq Kayani, Defence Minister Ahmed Mukhtar, intelligence chief Lieutenant General Ahmed Shuja Pasha and President Asif Ali Zardari.

The former CIA director, who flew out of Islamabad Friday, was also seeking Pakistan's cooperation on Obama's new strategy to turn around the war in Afghanistan, which involves sending more troops but drawing down forces starting in July 2011.

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