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On October 17, 1961, under the orders of then Paris police chief Maurice Papon, police attacked a demonstration by 25,000 pro-National Liberation Front (FLN) Algerians protesting against a curfew imposed on Algerians.
The march was repressed "brutally, violently and in blood", Macron's office said in a statement, adding that some 12,000 Algerians were arrested, many were wounded and dozens killed.
Macron attended a ceremony commemorating the anniversary at the bridge at Bezons, west of Paris, from where some Algerians had started their march and where many bodies were recovered from the Seine.
"He admitted the facts: the crimes committed that night under the authority of Maurice Papon are inexcusable for the Republic," the Elysee Palace statement said.
The massacre, which took place during the war against French rule in Algeria, was long denied or concealed by French authorities. The first commemorations of the event were organised in 2001 by the mayor of Paris.
The precise number of victims was never established, with some historians putting it at over 200 dead.
This year's commemoration takes place amid diplomatic tensions between Paris and Algiers.
Early this month Algeria recalled its ambassador to Paris, citing comments attributed to Macron, who was quoted in the Le Monde newspaper as saying Algeria's rulers had rewritten the history of its colonisation based on "a hatred of France".