Hundreds fled or were pushed to the harsh border area between Tunisia and Libya after racial tensions flared last week into violence against migrants from sub-Saharan African countries.
Dozens of other migrants were pushed towards Tunisia's southern border with Algeria.
Beity, a non-governmental organization helping victims of gender-based violence and discrimination, called on aid workers, charities and public institutions to "coordinate efforts and pool resources" for the stranded migrants.
"We have been witnessing for days ... a real manhunt going on" in Sfax, Beity said in a statement, denouncing "security threats" for migrants and "their expulsion and deportation" towards the Sahara desert.
The crackdown on migrants in Sfax, a departure point for many hoping to reach European soil, erupted after the funeral of a 41-year-old Tunisian man who was stabbed to death on July 3 in an altercation between locals and migrants.
Tunisia has seen a rise in racially motivated attacks after President Kais Saied in February accused "hordes" of undocumented migrants of bringing violence, and alleging a "criminal plot" to change the country's demographic make-up.
There are at least 450 migrants at the militarized buffer zone between Tunisia and Libya, near Ras Jedir, according to the Tunisian Observatory for Human Rights.
An AFP correspondent saw five buses passing by the area midday on Monday to take them to a school building in the Tunisian town of Ben Guerdane.
The Tunisian Red Crescent brought the stranded water and food over the past few days and evacuated the wounded, according to migrants at the site.
For those sent near the Algerian border, the situation is becoming increasingly difficult, witnesses told AFP.
"Please help us. If you can send the Red Cross here, help us, otherwise we will die," Mamadou, a migrant from Guinea who gave only his first name, told AFP by phone.
"There is nothing here. There's no food, there's no water."
About 30 migrants have been abandoned to fend for themselves in a desert area near the Algerian village of Douar El Ma, close to the Tunisian border, he said.
Aid group Refugees International said in a statement Tunisian authorities have "violently arrested, transported and expelled hundreds of black migrants and asylum seekers."
It noted some of those expelled have legal status in Tunisia and are registered with the United Nations refugee agency UNHCR.