"From the start Detlev Mehlis said that he would only stay six months (in charge of the commission of inquiry) and he has informed me that he cannot stay (beyond that date)," Siniora told reporters on Wednesday.
"Negotiations are now going on at the UN Security Council with the Secretary General (Kofi Annan) to appoint a successor," he said.
Sources said last week that Annan was attempting to persuade Mehlis to stay on with the inquiry at a crucial stage as officials interrogate Syrian officials in connection with the 14 February bomb blast that killed al-Hariri.
Mehlis, who took up his post in June, has himself emphasised that his employer is the German government and he has work waiting for him at home.
Siniora also tried to reassure Lebanon there was no cause for concern in Mehlis leaving when his commission’s mandate expires on 15 December, amid press complaints the magistrate was leaving an inquiry that could still take years.
"Mr Mehlis will still be available in case of need ... Stay calm, Lebanon is solid and every problem can be resolved," he said.