"Racism has no place in our democracy," said France's prime minister, reacting to the outburst.
A French parliament session was suspended on Thursday after the turmoil caused by a far-right MP shouting "back to Africa" as a black colleague posed a question on migrant arrivals to the government.
Carlos Martens Bilongo of the leftist France Unbowed party (LFI) was questioning the government on the request by the SOS Mediterranee NGO for Paris's help in finding a port for 234 migrants rescued at sea in recent days.
"Go back to Africa!" interrupted Grégoire de Fournas, a newly-elected member of the far-right, anti-immigration National Rally (RN).
The outburst sparked yells of condemnation and chants demanding de Fournas leave the assembly.
In French, the pronouns "he" (il) and "they" (ils) — as heard in the 'Qu'il retourne en Afrique' phrase uttered by De Fournas — are pronounced the same, suggesting that he might have been targeting Bilongo directly.
The Speaker of the Parliament, Yael Braun-Pivet, was eventually forced to suspend the session.
Bilongo said the comments were "shameful".
"Today it's come back to the colour of my skin. I was born in France, I am a French MP," he added.
A member of Macron's entourage said the president was "hurt" by the "intolerable" comments, while Prime Minister Elisabeth Borne urged the assembly to sanction the far-right MP, adding that "racism has no place in our democracy".
Le Pen backs her MP
The far-right leader of RN, Marine Le Pen, backed her MP on Twitter by saying, "the controversy created by our political opponents is obvious and will not fool the French people".
Le Pen challenged Macron in this year's presidential vote and then led her party to its best-ever performance in subsequent legislative elections, with 89 MPs.
The far-right party was founded by her father, Jean-Marie Le Pen, but his daughter claims to have overhauled the former National Front into a mainstream force, despite critics who say the changes are only cosmetic.
De Fournas later defended his comment, telling BFM television that the National Rally wants a halt to all illegal immigration after a surge in the number of people trying to reach France from Africa in recent years.
He accused France Unbowed opponents of "manipulation", and his party also denied any personal attack against Bilongo, a teacher of Congolese heritage who was born in Paris.
De Fournas later apologised to Bilongo for "the misunderstanding my comments caused," and in case Bilongo was hurt by them.
Macron's party refuses to show up for further sessions
Jordan Bardella — a favourite to take over officially from Le Pen at this weekend's RN congress — insisted the MP had meant the return of boats to African ports and accused LFI and the government of "extreme dishonesty".
LFI leader Jean-Luc Melenchon tweeted that the comments were "beyond intolerable" and that the deputy should be kicked out of the National Assembly.
A parliamentary committee will meet Friday to discuss the incident, which could see de Fournas punished with a temporary exclusion from the Assembly.
Macron's centrist Renaissance party will refuse to attend further sessions unless the council issues a "heavy penalty", its vice-president in parliament Sylvain Maillard said on Twitter.
The ruling party failed to win an overall majority in the legislative elections, leading to tensions as Macron's government seeks to push key bills through the legislature.
RN MPs have been involved in earlier controversies during the latest term. First, the oldest member of the National Assembly José Gonzales praised French Algeria and its colonial rule on 28 June.
During a recent session, two RN deputies lashed out at the government, calling the Minister of Economy Bruno Le Maire a "coward" and the Minister of Education Pap Ndiaye a "communitarian".
These invectives led to sanctions by the President of the National Assembly, which are also to be debated by the institution's bureau.
De Fournas, a wine grower in the Nord Médoc, is in his first term of office at the age of 37. He had not participated in any rows until now in the Palais Bourbon, where he sits on the Economic Affairs Committee.