More planes were expected to take off later on Tuesday, some loaded with illegal immigrants from Mali.
About 600 Senegalese and another 606 Malians were being temporarily housed in Oujda, a town bordering Algeria, ahead of deportation.
The immigrants, many of whom initially slipped across the border from neighbouring Algeria, have been using Morocco as a gateway to Europe, making their way north in a bid to reach Spanish enclaves there that would give them a foothold on European soil.
The Royal Air Maroc Boeing 737 filled with Senegalese took off at about 0915 GMT.
Morocco has come under fire for its handling of recent attempts by immigrants to rush barbed-wire fences at two Spanish enclaves in northern Morocco.
Nearly a dozen immigrants have died in their attempts to get to the other side, some with gunshot wounds.
Use of force
However, Morocco's Communications Minister, Nabil Benabdallah, defended the use of force in dealing with a problem that he said rightfully belongs to the international community.
Morocco is blamed for abandoning
immigrants in the desert
Morocco is in a no-win situation, Benabdallah said on Monday.
Previously it was criticised for not doing enough to stem African immigration.
"Then, when we used other means, including force, we created some humanitarian problems. It is not possible to fight this problem without causing humanitarian problems," he said.
The drama in the North African kingdom has highlighted the larger problem of illegal immigration that has haunted Europe for decades.
UN Secretary-General Kofi Annan said in Geneva on Monday that he suspected the issue of people moving across borders "will consume far more of our energy in the years ahead".
He said there were about 200 million people living outside their countries today. "What is important is that we don't make a futile attempt to prevent people from crossing borders. It will not work."
Amnesty International on Tuesday criticised the European Union over its refugee policy, claiming the 25 member states were focused on keeping people out instead of providing proper protection.
"The overall direction of EU policy appears to be far more geared toward keeping people out of the EU at all costs," said Dick Oosting, director of the human rights group's EU department.
Amnesty International criticised
the EU over its refugee policy
EU justice and home affairs ministers were to discuss the issue of illegal immigration during a meeting in Luxembourg on Wednesday.
Morocco, meanwhile, was taking a tough act against the immigrants using this North African kingdom as a stepping stone to a better life.
Benabdallah, the communications minister, denied claims that Morocco abandoned some immigrants in the desert.
However, he also said the numbers involved were so large that he could not say for certain if all received water and food.
Medecins Sans Frontieres, or Doctors Without Borders, said Moroccan authorities last week abandoned 600 to 700 immigrants in a desert area near the border with Algeria after Spain expelled them from Melilla and Ceuta.
The aid group said it treated at least 50 for injuries, including some apparently caused by rubber bullets and beatings.
Complicating the matter is a camp set up by immigrants on the Algerian side of the border. About 1500 to 2000 of them are waiting there to cross, local Algerian reporters who visited the camp said.