A presidency official said the plan - for which Macron set the goal of becoming operational "this summer" - "was not possible at the moment" because of security in Libya.
Instead, France would study the feasibility of setting up migrant "hotspot" centres in Niger and Chad, and aim to open similar sites in Libya "in the short term".
Macron had said earlier Thursday that he wanted to set up processing centres in Libya "to avoid people taking crazy risks when they are not all eligible for asylum".
Speaking during a visit to a refugee shelter in Orleans in central France, Macron said the plan would be put in place "this summer", with or without other EU countries.
Libya is the main launchpad for African migrants trying to reach Europe across the Mediterranean in boats operated by smugglers, rickety vessels that frequently sink.
"We have between 800,000 and a million people in Libya - in camps, hangars, there's not even a minimum of humanity," Macron said.
He said other European countries were "very reticent" to set up registration centres, adding: "We'll try to do it with Europe but we in France will do it."
But his announcement seemed to take the European Commission by surprise and Human Rights Watch expressed serious concerns about the plan.
Judith Sunderland, HRW's Associate Director for Europe, said: "It carries the risk of human rights abuses and loss of dignity for the people involved."
Hours after the original announcement, a French presidency official explained that "Libya is not possible at the moment, but it could be possible in the short term. Does that remove the ambition to create this sort of centre in Libya? No.
"The important thing is to ensure the security of people who will work there and of the migrants," the official added.
Libya is rife with lawlessness since the 2011 uprising ousted longtime dictator Moamer Kadhafi and created a power vacuum.
Macron's announcement came two days after he brokered talks in Paris between the leaders of the two rival authorities in Libya.
He said then that he hoped the ceasefire deal between the UN-backed Prime Minister Fayez al-Sarraj and Khalifa Haftar, the military commander based in the remote east, would stem the outflow of migrants from Libya.
Since January, more than 100,000 people have made the perilous voyage across the Mediterranean, according to the International Organization for Migration (IOM). Over 2,300 have drowned in the attempt.
The vast majority land in Italy, which has complained of a lack of solidarity from its neighbours in dealing with the influx.
Macron on Thursday phoned Italian Prime Minister Paolo Gentiloni to discuss events, a presidential aide said.
The two "shared a certain degree of optimism after the (Paris meeting), reaching very similar conclusions," the source said, adding that Macron also briefed Gentiloni on his plans for registration centres.
More shelters in France
France's new leader has taken an ambivalent line on migration.
During his campaign he was fulsome in his praise of German Chancellor Angela Merkel's open-door policy but his government has taken a hard line with young migrants sleeping rough on the streets of the northern French port of Calais
But in a speech on Thursday at a citizenship ceremony for families in the central city of Orleans, Macron adopted a more compassionate tone.
"I want no one in the streets or in the forests by the end of the year," he said, promising "dignified" accommodation for all those who made it to France while their cases were assessed.
He reiterated a pledge to slash the average processing time for an asylum claim from 18 months to six.
But he also warned that those who were fleeing poverty, rather than war or persecution, faced disappointment.
"No country can take all the economic migrants," he said.