PARIS, April 10 (Reuters) - The family of a witness in a U.N. probe into the killing of former Lebanese Prime Minister Rafik al-Hariri asked France on Thursday to explain what had happened to him after he disappeared from his French home.

Mohammed Zuhair al-Siddiq, a former Syrian intelligence officer, had been living in France but left the country on March 13, the French Foreign Ministry said on Thursday, prompting speculation about his whereabouts and his wellbeing.

The U.N. probe is a sensitive issue in Lebanon, where tension between pro- and anti-Syrian camps runs high. Hariri's killing sparked a worldwide outcry that forced the withdrawal of Syrian troops which had been in Lebanon for nearly 30 years.

"Our consul in Damascus today met the brothers of Siddiq, who gave him a letter asking for clarifications on their brother's fate," Foreign Ministry spokeswoman Pascale Andreani told reporters.

Asked about a newspaper interview in which Siddiq's brother said France facilitated his disappearance or "liquidated" him, Andreani said: "I formally deny the accusations you are referring to."

Lebanon's prosecutors believed Siddiq had an indirect role in the Feb. 14, 2005, killing of Hariri and 22 others, and they charged him with murder in October 2005.

Siddiq was arrested in a Paris suburb that month after an international arrest warrant was issued for him, but French judges rejected Beirut's extradition request because they received no guarantees he would not face the death penalty.

He was freed in 2006 and had been living in France. Andreani said threats had been made against him, which prompted the Foreign Ministry to inform local police of his presence.

Siddiq's importance to the U.N. probe is, however, unclear.

He was not under house arrest in France, and the prosecutor heading the U.N. investigation into Hariri's death, Daniel Bellemare, has said the U.N. team interviewed him but he never replied to an offer to enter a witness protection programme.

"He is not in our custody and I don't know where he is," Bellemare told reporters at U.N. headquarters in New York on Tuesday.

"As far as the impact of his disappearance (on the investigation), this will have to be assessed," he added.

Siddiq told investigators he had attended several meetings at a Beirut suburb to plan the truck bombing. A U.N. report in 2005, however, said DNA samples taken from Siddiq did not match evidence gathered from that location or the crime scene, and the reliability of his testimony has been called into question.

The head of the first U.N. investigation, Detlev Mehlis, implicated senior Syrian officials but his two successors, including Bellemare, have not repeated the charge. The Syrians have repeatedly denied any role.

Bellemare asked the U.N. Security Council on Tuesday for more time to pursue leads in the case.

Although the investigation was making steady progress, Bellemare told the Security Council there would be no indictments issued in the immediate future. (Reporting by Francois Murphy in Paris and Louis Charbonneau at the United Nations, editing by Mary Gabriel)

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