"These latest discriminatory chants from Paris Saint-Germain supporters are unacceptable," the LFP said on Sunday.
"The whole of professional football has been working for several seasons to ban homophobic behaviour and chants from stadiums."
The LFP said its disciplinary committee would investigate the incident at the match, which Paris Saint-Germain won 4-2.
The chants, mainly from PSG's hardcore 'ultras' fan base, lasted around 10 minutes and were directed against Marseille ahead of the French champions' clash with their arch rivals in the southern port city next weekend.
The stadium announcer made two appeals over the tannoy for them to stop.
Last season PSG were ordered by the LFP to close the ultras' stand for one game over a similar incident.