"I understand the feelings that this arouses, I respect them. But I want you to understand the role that I have. My role is to calm things down, as I am doing here, but at the same time it is to protect these rights," Macron said. "I will always defend in my country the freedom to speak, to write, to think, to draw."
"That doesn't mean that I personally support everything we say, think, draw, but ... I consider that it is our vocation to protect (these freedoms and human rights) and also to protect the sovereignty of the French people."
The interview will air on Sunday, but Macron posted the full, French-language interview on his YouTube channel.
France has been on edge since an attack in September outside the former offices of satirical magazine Charlie Hebdo, which republished cartoons of the prophet in a recent edition.
Macron emphasized in the interview that the cartoons were not the work of the French state. He said political leaders had distorted the truth, leading people to believe the French government was responsible for the caricatures.
"The caricatures are not a governmental project, but emerged from free and independent newspapers that are not affiliated with the government," he added.
Macron told Al Jazeera that his comments that Islam was facing a crisis were referring to the extremist elements that also threatened mainstream Muslims.
"What I wanted to say is very clear, that today there are people in the world that distort Islam and who kill in the name of a religion that they claim to defend. They slaughter," he said. "Today there is violence practised by some extremist movements and individuals in the name of Islam."
"Of course this is a problem for Islam, because Muslims are the first victims. More than 80% of the victims of terrorism are Muslims. And this is a problem for all of us."
He defended France's secularism, but said the concept was often misunderstood. He said people were completely free to practise their religion, and no matter their beliefs, they were treated equally in France.
Macron also said religious and political leaders who failed to condemn the violence were partly responsible for encouraging the attacks, and called for support in condemning attacks in France.
Macron defended his plans for a bill to combat Islamic extremism, saying that it would help defend the Muslim community in France. He also said the legislation would target people who promote extremism and keep the Muslim community integrated in French society.
"We are going to prevent children from dropping out of school, we are going to prevent financing linked with terrorist activities ... And above all, we are going to ensure ... that everyone, whatever their religion ... fully respects the laws of the French Republic."
In this same effort, he said France would also reform its housing and education policies and work to empower the disenfranchised.
He called on the Islamic community to help combat the scourge of violent and extremist groups that hijack Islam to commit inhumane acts, citing "Islamic State," Islamists in the Sahel region, the Taliban and al-Qaida.