Prime Minister Joseph Muscat confirmed that Zaidan was in Malta on a refuelling stop and the two met briefly.
Dr Muscat did not say where the Libyan PM was headed and the meeting between the two was more of a sign of personal friendship.
The PM said that Malta is following closely what is happening in Libya.
The Associated Press reported that Libya’s ousted prime minister has left the country despite a ban on travel, hours after parliament removed him from office in a no-confidence vote.
Officials in Tripoli on Wednesday could not confirm the departure of Ali Zeidan, Libya’s first democratically chosen leader who had struggled for 15 months to stem the country’s spiraling descent into chaos.
But Maltese Prime Minister Joseph Muscat told state-owned television that Zidan had made a brief stop-over on the Mediterranean island late on Tuesday, before travelling on.
The Western-backed Zeidan was ousted in a parliament vote on Tuesday as Libya faces a series of crises, including an escalation over oil ports seized by an eastern militia.
Soon after parliament voted, Libya’s general prosecutor banned Zeidan from travel pending an investigation into corruption allegations.