Faced with the prospect of being blocked by the fishermen in Zarzis, the ship, the C-Star, moved up the Tunisian coast, and was expected by opponents tracking its path to try to land at either Sfax or Gabes on Monday.
Chartered by extremist group "Generation Identity", the C-Star passed through waters off Libya on Saturday.
It briefly tailed the Aquarius, operated by French group SOS Mediterranee, one of several NGO boats conducting search and rescue operations in an area notorious for deadly migrant boat sinkings.
"If they come here we'll close the refuelling channel," Chamseddine Bourassine, the head of the local fishermen's organisation, told AFP.
"It is the least we can do given what is happening out in the Mediterranean," he added.
"Muslims and Africans are dying."
An official at the port, who asked to remain anonymous, said: "What? Us let in racists here? Never!"
The C-Star headed straight from Cyprus to Libyan waters after being discouraged from attempting to dock en route in Greece and Sicily, with authorities concerned about the prospect of protests.
Their boat was held up for a week in the Suez Canal by Egyptian authorities looking for weapons.
Then, after it landed in the Cypriot port of Famagusta last month, several of its crew jumped ship and asked for asylum in Europe -- exactly the kind of thing the mission was set up to prevent.
The C-Star crew say their main goal is to expose collaboration between NGO rescue ships and the traffickers who launch boats from Libya packed with migrants.
Humanitarian groups say Generation Identity is engaged in a publicity stunt and that any attempt to turn migrant boats back to Libya would be potentially very dangerous and illegal under international law.
Over 10,000 have died en route and serial sinkings have resulted in privately funded or charity-run boats joining a multinational search and rescue operation coordinated by Italy's coastguard.
NGO boats have rescued around one third of the nearly 100,000 people picked up this year, but their relations with Italy have become strained as pressure to stem the flow of migrants has mounted.
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