Islamabad also was required to have made progress toward stopping al Qaida, the Afghan Taliban, the Haqqani network and allied Pakistani extremists “from operating in the territory of Pakistan” and staging attacks in neighboring countries. It also must move toward shutting down “terrorist” bases in the tribal areas and other parts of its country.

Clinton didn’t disclose which specific prerequisites Pakistan failed to meet. Those details were classified.

It’s the first time that the Obama administration has waived the requirements, something the Bush administration did six times for democracy-related sanctions.

Until now, Clinton had certified Pakistani compliance even though U.S. commanders in Afghanistan and other U.S. officials had for years charged the Pakistani army and the ISI with supporting the Afghan Taliban and the Haqqani network. In September 2011, Defense Secretary Leon Panetta and retired Adm. Mike Mullen, the former chairman of the Joint Chiefs of Staff, explicitly accused the ISI of aiding Haqqani network attacks on U.S. targets in Afghanistan, including a strike against the U.S. Embassy.

Four days before she notified Congress she was waiving the conditions, Clinton decided – under pressure from Congress – to add the Haqqani network to the U.S. list of terrorist organizations. The Pakistani military, which for years has rejected U.S. demands that it move against the Haqqanis’ stronghold of North Waziristan, thinks that the group should participate in any settlement to the Afghan war.

Clinton’s decision to waive the conditions comes as the United States and Pakistan strive to rebuild a relationship battered by a series of events that began when a CIA contractor shot dead two alleged thieves in Lahore in January 2011. Ties also have worsened over intensified CIA drone strikes, which Pakistan charges are violating its sovereignty and killing civilians.

U.S. commandoes killed Osama bin Laden in May 2011 in Pakistan in a raid kept secret from the Pakistani army, embarrassing and enraging its commanders, and last November, U.S. forces in Afghanistan inadvertently killed 24 Pakistani soldiers in a border post, prompting Pakistan to close the NATO supply routes that the United States needs to ship military equipment out of Afghanistan.

The sides agreed in July to reopen the routes in a first step towards rebuilding ties, which Washington considers vital as the pullout of international forces from Afghanistan continues. It’s also seeking Pakistani help in trying to draw the Afghan Taliban into peace negotiations.