The change in Pakistan's political climate has left the United States in a spot.
Only last week did the US officials reach a hushed understanding with Musharraf to intensify secret strikes against suspected terrorists by pilotless aircraft in Pakistan, New York Times has reported quoting senior officials in the administration.
But the sudden change in political circumstances after the key polls in Pakistan has US worried about the recently stepped-up operations to root out terror elements, the article said.
The new deal has in fact allowed the US to strike by armed Predator surveillance aircraft launched from a secret base in Pakistan. But that may not happen, the paper says, after the reversal in fortunes of Musharraf's party.
The paper says President Bush's national security advisers had a series of meetings with top Pakistan leaders after which the US forces could attack suspected Al Qaeda and Taliban fighters.
The change allows American military commanders greater leeway to choose from what one official who took part in the debate called "a Chinese menu" of strike options, the paper claimed.
The new deal has given the US to strike convoys of vehicles that bear the characteristics of Al Qaeda or Taliban leaders on the run, without even confirming the target.
Such an outright operation was kept secretly earlier to avoid embarrassing President Pervez Musharraf politically, the article says.
Musharraf has been accused by political rivals of being too close to the US.
The paper says the US base in Pakistan has a handful of Predators -- unmanned aircraft that are controlled from the United States. Two Hellfire missiles from one of those Predators are believed to have killed a senior Qaeda commander, Abu Laith al-Libi, in northwest Pakistan in January though a senior Pakistani official said his government had still not confirmed that Libi was among the dead.
The new deal, the paper says, came Mike McConnell, the director of national intelligence, and General Michael V. Hayden, the CIA director took a trip to the United States.
The officials are learnt to have met with Musharraf and new army chief Ashfaq Parvez Kiyani and offered a range of increased covert operations.
But now the deal is in a spot. US top officials are concerned that these arrangements could come under review or be scaled back by the winners of Pakistan's parliamentary elections. The two winning parties have already indicated that they want to enter talks with Pashtun tribal leaders who opposed Musharraf.
Xenia Dormandy, the director for South Asia at the National Security Council until 2005, told the paper that the militants would probably continue to gain strength if such a situation arose.
The paper says other administration officials warned not to read too much into initial comments from Asif Ali Zardari, the leader of the Pakistan People's Party and widower of former prime minister Benazir Bhutto, about reaching accords with the tribal leaders. Zardari, they noted, has made clear that he wants to defeat terrorism.
"In the short term, there will be some confusion and some hiccups," Henry A Crumpton, a former top State Department counterterrorism official told the paper.
"But in the medium and longer term, there will be continued and perhaps even closer cooperation, because of our mutual interests."
