"Following the latest restrictions imposed by the Qatari authorities, Royal Air Maroc [RAM] regrets to inform customers of the cancellation of their flights operated by Qatar Airways," the airline said in an emailed statement.
The cancelled flights impact "2,100 passengers," a separate source, who wished to remain anonymous, told AFP, adding that 23 other flights operated by RAM are still planned.
In Doha, Moroccan supporters who arrived on the first of the special flights said on Tuesday afternoon that the Moroccan football federation had promised them match tickets on arrival at the airport, but that these tickets had not yet materialized.
On December 2, Qatari authorities dropped a previous requirement that arrivals in the country present a match ticket upon entry.
But a message posted by Hamad International Airport on Wednesday morning urged supporters "not to go to the two airports (of Doha) until they have obtained tickets for the upcoming matches".
"We remind supporters that Hamad International Airport in Doha is not the official site for obtaining tickets for World Cup matches," the message added.
Videos posted on social networks showed groups of Moroccan supporters blocked by Qatari security officials at the airport.
RAM said it would reimburse air tickets and apologized to customers.
The RAM spokesperson did not immediately respond to Reuters request for comment. Qatar Airways did not immediately respond to Reuters request for comment.
This report was prepared with data from Reuters and Agence France-Presse.