The American ambassador who has told President Obama he has serious concerns about increasing troop levels in Afghanistan urged the Bush administration repeatedly not to withdraw forces while he was the top military commander there. 

Army Lt. Gen. Karl Eikenberry also forcefully pressed NATO to contribute more troops to the war while keeping a broad focus on threats both in Afghanistan and Pakistan when he was commander of Combined Forces, Command Afghanistan.

Eikenberry's recent concern about sending more troops to Afghanistan -- confirmed late Thursday by White House officials -- seems to speak to his eroding confidence in the credibility of the Hamid Karzai-led Afghan government. 

"Ambassador Eikenberry expressed his reservations about troop increases to the president while Afghanistan's political situation remains unclear," a U.S. official told Fox News. "He is the ambassador to the country and it is purview to do that."

Multiple classified cables he sent to Washington over the past week suggest Eikenberry, now the U.S. ambassador to Afghanistan, harbors deepening concerns about whether the Afghan government is so unstable as to make troop increases ineffective. 

Eikenberry consistently has put a premium on the need to strengthen state institutions in the country, tying the power of the Taliban to the weakness of the government. But one administration official said Eikenberry stressed the point this week that the administration should step cautiously in planning for any troop buildup while there are still so many questions surrounding Karzai. 

"(Eikenberry's concern) has all to do with the Afghan government," said Malou Innocent, foreign policy analyst at the Cato Institute. "I think his hesitancy at least is an implicit recognition that the administration is seriously rethinking policy." 

Innocent said Eikenberry's cables reflect a concern that more troops would only exacerbate the "dependency" of the Afghan government on U.S. forces, and that Karzai's win by default following a fraud-marred election only adds to the perception of Kabul as an "illegitimate government" among the Afghan people. 

Eikenberry reflects just one wing of Obama's inner circle of war advisers. Gen. Stanley McChrystal and other military officials are calling for a significant troop increase to secure the Afghan population and keep the Taliban from gaining ground, regardless of corruption in Kabul. Secretary of State Hillary Clinton, Eikenberry's boss, reportedly supported an alternative deployment of 30,000 more troops.

State Department Press Secretary Ian Kelly said Thursday that Eikenberry is not at odds with Clinton, and merely was offering advice in a confidential way.

"The role of -- of the secretary and Ambassador Eikenberry in this is to provide their point of view. This will all go into the deliberation that the president is making right now," Kelly said. "Where the secretary comes down on this issue, that is her private, confidential advice for the president, and I'm going to honor that."

He declined to entertain the premise that Eikenberry's consult was leaked to give the president cover to reject more troops.

Though Eikenberry has long sent warnings about problems in Kabul, he was at the forefront of calls to crack down on the Taliban with troop strength when he held the job that is now McChrystal's. 

The New York Times reported in 2007 article that it was Eikenberry who, as the American commander at the time, convinced the Pentagon to abandon a planned 2005 troop reduction. Eikenberry warned that troops were needed to fight a resurgent Taliban and that the Afghans would doubt U.S. "staying power" if they withdrew troops. 

In early 2007, shortly before he left his military command, Eikenberry urged the Bush administration to keep on 1,200 soldiers through the end of the year, even though they were scheduled to be deployed to Iraq. He again cited a looming Taliban offensive as the reason. 

Back then, forces were stretched much thinner, with Iraq still the central battlefield for U.S. forces, making every battalion all the more valuable to Eikenberry. The U.S. troop level is now three times as large as it was then. 

Eikenberry's emerging concerns in late 2009 speak to new doubts about a war he has staunchly defended. 

"The United States will not leave Afghanistan until the Afghan people tell us the job is done," he was quoted as saying in late 2006. "The war on terrorism began here in Afghanistan and it continues today. We must never forget that." 

He repeated that point in a September 2006 interview with NPR. 

"We'll know when we've won when the Afghan people tell us that it's time for the United States to leave," he said. He defined that point as a time when the governance, security and economy of that country are stable enough to ensure "international terrorism has no place to live." 

He defined the U.S. mission as a war against Al Qaeda and the Taliban, and a quest for reform in the Afghan government. 

Aaron David Miller, a former State Department adviser now attached to the Woodrow Wilson International Center for Scholars, said Eikenberry's latest warnings should be taken seriously, considering his experience in the region. 

"You've got to listen to the guy. You really do," he said. 

Among other roles, Eikenberry has also served as U.S. security coordinator and chief of the Office of Military Cooperation in Kabul, Afghanistan, as well as director for strategic planning and policy for U.S. Pacific Command and deputy director for strategy, plans and policy on the Army Staff. 

Miller said the United States needs to assess its goals in the country, but argued that eliminating the terrorist threat needs to take precedence over changing the Afghan government. 

"I would argue we need to think through very carefully and clearly what kind of resources we need to do that," he said. "We do not want an investment trap of a 20- or 30-year period with 100,000 American forces on the ground." 

Miller called the lengthy deliberations "necessary and wise." 

But others have grown increasingly frustrated with the process. Senate Republicans on Wednesday called for Obama who has been mulling a decision for more than two months, to reach one soon for the sake of the security of the troops who are already there. 

Obama rejected all the options for troop increases given to him at a strategy session Wednesday, and is now pushing for revisions to clarify how and when U.S. troops would turn over responsibility to the Afghans, a White House official told Fox News. 

"This is like a slow-motion train wreck, watching this decision-making process," said John Bolton, former U.S. ambassador to the United Nations under the Bush administration. 

FoxNews.com's Judson Berger, Fox News' Justin Fishel and Mike Emanuel, and The Associated Press contributed to this report.