Keith Schembri is travelling abroad on Thursday after notifying police that he would be taking his family overseas on a "getaway".
Sources confirmed that the police had been contacted by Mr Schembri’s legal team, who informed the corps that the former chief of staff was planning a trip to Italy.
Mr Schembri is a person of interest in the investigation into the assassination of journalist Daphne Caruana Galizia.
He was held under arrest and interrogated last month but was released 48 hours later without charge.
He was seen on Thursday evening at the VIP lounge of Malta International Airport.
Sources close to the murder investigation expressed concerns about Mr Schembri’s travel out of the country at such a delicate stage of the investigation.
However, the sources also pointed out that since Mr Schembri had been released and not placed on police bail, he was free to do as he pleased.
MEP David Casa said in a tweet it was absolutely unbelievable that instead of interrogating Mr Schembri, the police gave him permission to fly out on holiday.
Chief investigator Keith Arnaud told the court in recent days the police have been unable to trace Mr Schembri's phone and that the former chief of staff had refused to give his passwords on grounds that his email accounts contained sensitive government information.
Mr Schembri had also been arrested after giving a statement to the police detailing what he knew about a phantom job given to the alleged middleman in the Caruana Galizia murder plot.
Widely credited as being the brains behind Labour’s seemingly invincible electoral machine and strategy, Mr Schembri resigned last month after it emerged that he was being questioned in connection with the murder case.
Mr Schembri had previously faced accusations of money laundering as well as having opened a secret company linked to 17 Black, which was owned by Yorgen Fenech, the man who now stands charged with the assassination.
Amended on December 28 - A previous version of this article had erroneously stated that Mr Schembri had been granted permission to travel abroad by the police.