The incident came as President Emmanuel Macron's government is promising a new crackdown on immigration amid accusations of failing to stem new arrivals or deport those whose residency requests are denied.
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.
"They should go back to Africa!" interrupted Gregoire de Fournas, a newly elected member of the far-right, anti-immigration National Rally (RN).
The outburst sparked yells of condemnation, not least because in French the pronouns "he" and "they" are pronounced the same, suggesting that de Fournas might have been targeting Bilongo directly.
National Assembly speaker Yael Braun-Pivet suspended the session after demanding to know who had made the comment.
"Racism has no place in our democracy," responded Prime Minister Elisabeth Borne, urging the assembly to sanction the far-right MP.
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 a "manipulation" and his party also denied any personal attack against Bilongo, a teacher who was born in Paris.
A parliamentary committee will meet Friday to discuss the incident, who 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.