Clinton's visit is the first by a Cabinet-level U.S. official to Libya since Moammar Gadhafi was driven from power nearly two months ago.
Clinton met with top officials of the National Transitional Council during her unannounced, 5-hour visit, The Washington Post reported.
"I am proud to stand here on the soil of a free Libya," Clinton told the interim Libyan leaders. "This is Libya's moment. This is Libya's victory and the future belongs to you."
State Department aides said Clinton, who also was to hold a town hall-style meeting, intended to reassure Libyan leaders of U.S. support as the country addresses challenges such as restoring basic services and locating thousands of missing surface-to-air missiles.
Clinton and transition government leaders will discuss "how we set the table for a long-term, completely different partnership between the United States and Libya that is deep and broad," a senior State Department official told reporters.
Clinton brought an increase in non-military aid, which has totaled more than $130 million since the start of the Libyan uprising, the Post said. The State Department also boosted funding and staffing levels to help Libyan officials recover and destroy conventional weapons from Gadhafi's munitions depots, including thousands of shoulder-fired, anti-aircraft missiles.
Clinton also was expected to announce financial assistance to help Libya provide long-term care to some of the country's estimated 15,000 war wounded.
Meanwhile, NATO officials in Brussels said while the organization's military mission in Libya, called Operation Unified Protector, is winding down, it is "premature" to set a timetable for ending it, the U.S. Defense Department said in a release.
"We are very close to the end, but there are still threats to the population," NATO deputy spokeswoman Carmen Romero told reporters in Belgium.
"And as long as these threats persist, we will continue with our operation."
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