Career diplomat Joe Pirotta, Malta's consul to Benghazi, had to be evacuated following threats to his life.
He was flown out of Libya yesterday, a day before Prime Minister Joseph Muscat travelled to Tripoli for a brief meeting with his counterpart Ali Zeidan this afternoon.
Dr Muscat's visit, however, was unrelated to the incident and was planned before Dr Pirotta received the threats, a spokesman for the Office of the Prime Minister said.
"A credible threat on Dr Pirotta's life was received and a decision was taken to evacuate him as a precaution," the spokesman said.
It is not yet clear whether Dr Pirotta, who served at the consulate almost uninterruptedly, even during the civil war, will be posted elsewhere and replaced in Benghazi.
Fielding questions at a press conference, following a meeting with Mr Zeidan, Dr Muscat was asked by Tripoli-based newspaper Al Ahrar about the bureaucracy that Libyans faced when trying to obtain visas to travel to Malta.
The Maltese consulates in Libya have been facing continued criticism over delays in the issue of visas, largely due to the offices being overwhelmed. However, it could not be ascertained whether the threats to Dr Pirotta were related to this problem.
During yesterday's press conference, Dr Muscat said the government was well aware of the complaints being made and has been working on a plan to address them.
"I will not give deadlines at this stage but I am sure that in the coming weeks we will be able to have a new system that strikes a better balance between security needs and the need to welcome Libyans wanting to travel to Malta," he said.