In an interview in Algiers with private owned TV Echourouk News, Macron said that colonisation was "genuinely barbaric, and constitutes a part of our past that we have to confront by also apologising to those against whom we committed these acts".
"France had installed Human rights in Algeria but has simply forgotten to read them", he added.
His rivals on the right for the French presidency pounced on the comments.
Right-wing, far-right reactions
Les Républicains candidate François Fillon denounced what he called "this hatred of our history, this perpetual repentance that is unworthy of a candidate for the presidency of the republic".
Wallerand de Saint-Just, an official in Marine Le Pen's far-right National Front party, accused Macron of "shooting France in the back", while Gerald Darmanin, an ally of ex-president Nicolas Sarkozy, tweeted "Shame on Emmanuel Macron for insulting France while abroad".
It was not the first time Macron has touched on the livewire issue.
"Yes, there was torture in Algeria, but there was also the emergence of a state, or wealth, of a middle class," he told the magazine Le Point in October.
"This is the reality of colonialism. There are elements of civilisation and elements of barbarism."
Fillon has also been tripped up by his own comments on France's colonialism.
In August, he drew criticism for saying: "France is not guilty of having wanted to share its culture with the peoples of Africa".
Macron, however, remains the frontrunner for the second round on the presidential race, with 39 percent of those surveyed in the latest survey by pollsters Ipsos giving him a favourable opinion.
In the poll released by the magazine Le Point on Wednesday, Macron was followed by Socialist candidate Benoit Hamon, with 38 percent, while Fillon tumbled 18 percentage points to 25 percent, just behind Le Pen, on 26 percent.