By Missy Ryan
WASHINGTON (Reuters) - A political crisis in Pakistan may threaten not only the future of President Asif Ali Zardari but also keep pressure on an already tense relationship with the United States as it seeks to stabilize neighboring Afghanistan.
A scandal over a murky memo that warned the Pentagon of a possible military coup in Pakistan has highlighted historic tensions between the weak civilian government in Islamabad and the powerful military, whose help Washington needs to battle militants fueling violence in Afghanistan.
Pakistan's Supreme Court began hearings this week into who was behind the memo, keeping the spotlight on a controversy that has added even more strain to U.S-Pakistan relations. The affair also threatens to undermine Pakistan's wobbly democracy as the United States seeks to mend those ties.
"The memo-gate issue is likely to have negative repercussions on the U.S.-Pakistan relationship," said Lisa Curtis, a former CIA analyst and State Department official now with the Heritage Foundation think tank in Washington.
"Many in Washington policy circles believe that forces that wish to undermine democracy in Pakistan are behind the affair."
Zardari returned to Pakistan on Monday from medical treatment in Dubai to face questions over the memo that a Pakistani-American businessman delivered to the top U.S. military officer earlier this year pleading for U.S. help in staving off a military coup.
The businessman pinned the origins of the memo on Pakistan's former ambassador to Washington, Husain Haqqani.
Haqqani, who resigned at the height of the affair, denies the allegations. Zardari's position may protect him if the probe were to prove links to the memo but the scandal could still threaten to force him out of office.
The controversy comes at a particularly tense time as U.S. investigators prepare to unveil a probe into an incident in late November in which NATO aircraft killed two dozen Pakistani soldiers along the border with Afghanistan.
The Obama administration's response to "memo-gate" has been muted, perhaps in part reflecting resignation among U.S. officials to troubled ties with an uneasy ally for now.
The two countries faced a series of crises in 2011: the arrest of a CIA contractor, the unilateral U.S. raid that killed al Qaeda leader Osama bin Laden on Pakistani soil and the closure of NATO supply routes through Pakistan.
The U.S. State Department says the memo scandal is an "internal matter" for the Pakistani government. On Wednesday, Pentagon spokesman George Little, speaking generally about the U.S.-Pakistan relationship, said the United States was committed to pushing through difficult issues.
"It's not going to be easy but with a lot of work we think we can do it," he told reporters.
QUESTIONS ABOUT PAKISTANI MOTIVES
There are also doubts in Washington about how much turbulence Pakistan's fragile democracy can withstand and whether courts can conduct a fair trial in a charged climate.
"The fact that the Supreme Court has now been involved gives (the memo matter) extra importance and legitimacy," said Shujaa Nawaz, a Pakistan scholar with the Atlantic Council.
Pakistan's top court is now moving ahead with the petition, filed by Nawaz Sharif, Zardari's chief opponent, raising questions about the political motivations for the case.
Bruce Riedel, a former CIA and White House official who chaired President Barack Obama's 2009 review of U.S. policy on the region, said Sharif himself initiated a similar petition over a decade ago.
He recalled a 1999 meeting with Sharif's brother Shahbaz, who he said traveled to Washington to warn of what civilian officials at the time feared was a brewing military coup.
"It was an entire day spent at the Willard Hotel listening to Shahbaz talk about their fears that a military coup was coming and asking for American help to prevent it," he said.
"That's pretty much the charge (that) is being leveled against Ambassador Haqqani."
A coup did ultimately happen, in 1999, bringing General Pervez Musharraf to power until he resigned as president in August 2008.
(Reporting By Missy Ryan; Editing by John O'Callaghan)