Alexandre Benalla, a former campaign bodyguard who got a senior job after Macron's election victory last year, has been caught up in scandal since July when accusations emerged he had roughed up protestors.
Macron's office and Benalla have clashed this week over accusations that he may have used diplomatic passports after he was dismissed in August, which the foreign ministry said would be a crime.
This latest episode adds to a series of scandals that have discredited Emmanuel Macron's presidency.
On Thursday, French website Mediapart revealed Benalla was still travelling on two diplomatic passports that were issued in his professional capacity as President Macron's aide.
The following day, Foreign Minister Jean-Yves Le Drian referred the case to Paris prosecutor Remy Heitz.
A judicial enquiry has been launched against Benalla for "breach of trust".
Non restitution et utilisation d’un passeport diplomatique par Benalla: le parquet de Paris ouvre une enquête préliminaire après le saisie du Quai d’Orsay, faisant elle-même suite aux révélation de @Mediapart. pic.twitter.com/ckI9FZG4KbFabrice Arfi (@fabricearfi) 29 décembre 2018
Any use of these passports after he was dismissed "would be against the law", the Foreign Ministry warned in a statement.
According to the statement, Macron's campaign bodyguard was twice requested to return the passports .
But Benalla's entourage told reporters that the passports were returned to him after he was dismissed.
"He left them in his office at the Elysee, and then they were given back", a source close to Benalla said, accusing opponents of seeking to destroy his reputation.
His entourage refused to comment on how Benalla may have used the passports.
Investigative website Mediapart revealed that Benalla used the passports to enter several African countries as well as Israel in recent weeks.
"This is very serious. The president must reveal the truth about this ," said Laurence Sailliet, spokeswoman for the right-wing Les Republicans party.
The scandal comes at an inopportune time for Macron, who has faced weeks of violent 'yellow vest' protests against his government's policies.