ISLAMABAD (Reuters) - Pakistan has appointed a new chief for the Inter-Services Intelligence (ISI) Directorate, months after U.S. officials had questioned the reliability of the military’s premier spy agency in the war against terrorism.

Pakistan's army chief General Ashfaq Kayani speaks at the test-firing of a medium-range Shaheen-1 (Haft-IV) ballistic missile at an undisclosed location January 25, 2008. REUTERS/Stringer

A military statement issued around midnight Monday announced a major overhaul of Pakistan’s top brass by army chief General Ashfaq Kayani.

The reshuffle will be closely scrutinized by the intelligence community in the United States and neighbors in the region.

A September 20 suicide bomb attack that killed 55 people at the Marriott Hotel in Islamabad underscored concern al Qaeda-linked militants and Taliban fighters could destabilize the nuclear-armed Muslim nation of 170 million people.

Lieutenant-General Ahmed Shujaa Pasha, formerly head of military operations, has been appointed Director-General of the ISI, replacing Lieutenant-General Nadeem Taj.

Kayani, who had been ISI chief until a year ago, also replaced four of the nine corps commanders and appointed a new chief of general staff.

Often referred to by critics as a “state within a state,” the ISI is feared by neighboring Afghanistan and India, as well as Pakistan’s civilian politicians whose governments have been overthrown by military coups.

The ISI helped the United States eliminate hundreds of al Qaeda fighters after the 2001 attacks on U.S. cities.

But U.S. officials suspect that some Pakistani agents still view the Afghan Taliban and some jihadi groups as long term assets to gain leverage in Afghanistan and Indian Kashmir.

U.S. fears that the ISI might be playing a double-game came to a head after a suicide bomber killed 58 people outside India’s embassy in Kabul in July.

The New York Times reported then that U.S. officials also believed Pakistani agents tipped off militants ahead of missile strikes against Taliban and al Qaeda targets in Pakistan.

After halting prior notification and increasing missile strikes, the United States went a step further in early September, carrying out a commando raid on a Pakistani village on the Afghan border that provoked a storm of protest in Islamabad.

The United States has privately urged Pakistan’s six-month-old civilian government to exert more control over the ISI, according to officials who requested anonymity.

Prime Minister Yousaf Raza Gilani’s government made a botched attempt to bring the ISI under the ambit of the Interior Ministry in July, but backed off to avoid a backlash within the army.

While Kayani has been supportive of Pakistan’s return to civilian-led democracy, senior officials say he has made clear the army will look after its own affairs, while the government gets on with the business of running the state.

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President Asif Ali Zardari, according to the New York Times, met with Michael Hayden, director of the Central Intelligence Agency, during a visit to the United States in the past week.

“The ISI will be handled, that is our problem,” Zardari, the widower of slain two-time prime minister Benazir Bhutto, told the newspaper in an interview released Sunday.

Sworn in earlier this month, Zardari was scathing about the policies of his predecessor, former army chief Pervez Musharraf.

“We don’t hunt with the hound and run with the hare, which is what Musharraf was doing,” Zardari said.

In his previous post, Pasha oversaw offensives against militants in the tribal lands bordering Afghanistan, and deployments to guard against cross-border militancy.

He is expected to overhaul the ISI and heads of sections dealing with domestic politics and media have been replaced, according to officials.

“Two heads have been changed and some rapid reshuffling is expected soon, as these have been due for long time,” a senior military security official, who requested anonymity, said. Taj had been ISI chief for less than a year, having been promoted to the sensitive post by Musharraf, who was forced to quit as president in August to avoid impeachment by parliament.

Taj, who was seen as close to Musharraf, was appointed as commander of Gujranwala Corps rather than sidelined.