Detlev Mehlis, a German prosecutor, made no comment on his findings when he met Annan at the secretary-general's residence in Manhattan.
The report goes to the Security Council on Monday and Mehlis will address the 15-member body on Tuesday afternoon.
Mehlis expects to leave his post at the end of the year, but Lebanon has asked that the inquiry be extended for a further six months and the Security Council is likely to renew the mandate before it expires on Thursday.
In an interim report in October, Mehlis implicated senior Syrian officials and their Lebanese allies, including President al-Assad's younger brother, Maher, and his brother-in-law, Brigadier-General Asef Shawkat, Syria's chief of military intelligence, in the plot to kill al-Hariri in February.
Syria has denied the accusations and called the Mehlis report politically motivated.
After the interim report, the Security Council told Syria to co-operate fully with the investigating team or sanctions might result.
Mehlis (L) made no comment on
his findings when he met Annan
In an interview published in Lebanon's al-Mustaqbal newspaper on Saturday, Mehlis said he would ask Syria if UN investigators could question new Syrian witnesses in Vienna, but he did not identify them.
His investigators questioned five Syrian officials there last week in connection with the truck bombing that killed al-Hariri and 22 others in Beirut.
"We have so far reconstituted half the puzzle," Mehlis told the newspaper, which is owned by al-Hariri's family. "There are still dark corners that we are shedding light on, but the inquiry is progressing."
In Damascus, Walid al-Moualem, Syria's deputy foreign minister, said his government had cooperated fully.
"There is no cause for concern and no justification for the Security Council to take any measure against Syria, unless some want to punish us for cooperating in good will with the international investigation," he said.
Damascus has campaigned to discredit the inquiry after Hosam Taher Hosam, a Syrian witness, recanted his testimony last month and accused Lebanese officials of threats, bribery and
torture to induce him to testify falsely against Syria.
He said the inquiry's initial findings rested largely on his lies. But Mehlis said that his investigation did not depend on Hosam's testimony.