Mr Macron was speaking to MPs as criticism peaked at the French leader over his handling of the saga of the 26-year-old.
Last Friday, Mr Benalla was sacked for his violent behaviour towards street protestors during a May Day protest in Paris.
Speaking about the man’s actions, Mr Macron told his MPs on Tuesday: “If they are looking for the person responsible, the only one responsible is me and me alone.”
He then hit back at those criticising him for defending his security officer who worked with Mr Macron in the French Presidential election election campaign.
He said: “Alexandre Benalla has never had the nuclear code. Alexandre Benalla is not my lover.”
The French President’s poll ratings plummeted to record lows, after the public expressed their outrage as Mr Macron delayed taking action against his former security adviser, Mr Benalla.
France’s opposition MPs have accused the government of covering up the scandal and paralysing parliamentary debate.
The parliament also launched a series of investigative committees to question the interior minister, Paris police chief and other high-ranking Elysee security personnel.
Mr Macron said he was “shocked” by Mr Benalla’s behaviour, claiming that he had abused his trust.
He told his MPs: “What happened on May 1 is terrible, serious, and for me it was a disappointment and a betrayal.”
Mr Benalla was only sacked and taken into police custody last week, despite the incident occurring in May.
This came after Le Monde newspaper published the video, leading to Mr Benalla’s arrest two days later – more than two months after he attacked street protestors.
In the footage, Mr Benalla was seen wearing police riot gear and pulling protesters away from violent scenes, in chaotic footage posted to Twitter.
Mr Macron also lashed out at the press, insisting that the media was no longer finding the truth but instead publishing “rubbish”.
He said: “We have a press that no longer seeks truth.
“(The media) says look! Looped images of a scene (of Mr Benalla’s violence), which is unacceptable and which I condemn. But I would like to see the scene before, the scene after, the context, what happened.
“Are (the images) shown with the desire to seek the truth and to present facts in a balanced manner?”
The French President also denied giving Mr Benalla the code to France’s nuclear arsenal.
However, opposition leaders called out the president out for his lack of action against Mr Benalla, insisting he should explain himself to the French people or stand before a parliamentary committee to be questioned.
Éric Ciotti of Les Républicains party sarcastically tweeted about Mr Macron’s speech, saying that “prefers to explain himself to his own little caste rather than give explanations the French are waiting for”.