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The White House spokesman David Leavy said that Mr Clinton had briefly met the Chinese Ambassador in Washington, Li Zhaoxing, and signed a condolence book for the victims of the embassy bombing.
Mr Clinton wrote: "With profound grief and sincere condolences to the victims their families and the people of China," according to the spokesman.
He had also told the ambassador that the United States would carry out a full investigation into the bombing and would inform the Chinese people of its results.
The Chinese ambassador indicated that President Jiang was now ready to accept the phone call from Mr Clinton which he had refused earlier.
The conversation is expected to take place on Friday.
The BBC's Paul Reynolds reports from Washington that while Chinese anger may have subsided, it does not guarantee their co-operation in the diplomacy over Kosovo.
On Wednesday, German Chancellor Gerhard Schröder said he had made a formal apology to China on behalf of Nato for the alliance's bombing of the Chinese embassy in Belgrade.
Mr Schröder was the first leader of a Nato country to visit China since the alliance attacked the embassy in what it called a "tragic mistake".
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