The CIA briefed senior Pakistani officials this month on the connections between radical Islamist terrorists in the Taliban and al-Qaeda and Pakistan’s own intelligence service.  While Prime Minister Yousaf Gilani still publicly refutes the charge, the US showed evidence that, at the least, rogue elements within the ISI have maintained ties to the movement they helped install in Afghanistan after the Soviets retreated:

A top Central Intelligence Agency official traveled secretly to Islamabad this month to confront Pakistan’s most senior officials with new information about ties between the country’s powerful spy service and militants operating in Pakistan’s tribal areas, according to American military and intelligence officials.

The C.I.A. emissary presented evidence showing that members of the spy service had deepened their ties with some militant groups that were responsible for a surge of violence in Afghanistan, possibly including the suicide bombing this month of the Indian Embassy in Kabul, the officials said.

The decision to confront Pakistan with what the officials described as a new C.I.A. assessment of the spy service’s activities seemed to be the bluntest American warning to Pakistan since shortly after the Sept. 11 attacks about the ties between the spy service and Islamic militants.

The C.I.A. assessment specifically points to links between members of the spy service, the Directorate for Inter-Services Intelligence, or ISI, and the militant network led by Maulavi Jalaluddin Haqqani, which American officials believe maintains close ties to senior figures of Al Qaeda in Pakistan’s tribal areas.

The CIA hasn’t yet determined how deep the penetration has been within the ISI.  Certainly, no one would be terribly surprised to find it significant.  The ISI has always sympathized with the Taliban, if not al-Qaeda, and seen the radical Islamists as a partner.  At one time, the entire Pakistani government felt the same way.  Both Benazir Bhutto and Pervez Musharraf had supported the Taliban movement at various times, and Musharraf only severed his connections after 9/11.

This appears to be a warning from the CIA and the Bush administration to the Pakistanis.  The US has made no secret of its impatience with the Gilani government over their appeasement strategy with the terrorists.  The Haqqani network has grown more sophisticated and dangerous, and NATO wants an end to their activities in Afghanistan.   The US believes they operate successfully because of ISI assistance and want the Pakistanis to put an end to it.

That’s easier said than done.  The new civilian government tried to bring ISI under their control, but the military and the ISI stopped that attempt last weekend, as the Times notes.  Without Musharraf’s strong authoritarian power and will, the ISI has grown more independent and more dangerous than before.

The army has announced a new operation in Swat today, in which they have ended a peace deal that never took hold.  The Pakistanis want to show that they’re taking action, but the hit-and-miss nature of the operations suggests that they’re more interested in playing favorites among the competing terrorist groups than in eliminating terrorists altogether.  That may or may not start with the ISI, but at least the message looks clear from the CIA: clean up your own house, or we’ll clean it for you.