"No fishing activity from the European fleet will be tolerated and all boats operating in the area of the fisheries agreement are asked to leave national territorial waters on Wednesday before midnight," the Moroccan foreign ministry said in a statement following the decision in Strasbourg on Wednesday (14 December).
Under the old agreement, the Moroccan government allowed European fishermen to operate in the area in return for some €36 million per year.
The European Commission extended the deal in February, pending formal approval by the European Parliament. But MEPs ruled it did not take into account the interests of the local Sahrawi people, whose status has been in limbo ever since Morocco annexed the area in 1975.
"Morocco has no right, under international law, to sell the natural resources of Western Sahara. It follows, therefore, that the EU should not be paying Morocco for fishing rights in the waters off Western Sahara," said Scottish MEP Ian Hudghton of the European Free Alliance, a grouping in the assembly bringing together independence movements across Europe.
Spanish Green MEP Raul Romeva said: "The agreement is a shameful stain on EU foreign policy and it is time it was consigned to the past."
The decision to annul the pact, which comes into force immediately, "should not be seen as a hostile move towards our partners," said Finnish liberal MEP Carl Haglund, who led the rebellion.
For her part, EU fisheries commissioner Maria Damanaki said the European Commission would respect parliament's decision.
She added that a replacement deal might be difficult to achieve, however. "We don't know if a new fisheries protocol with Morocco is possible," she said in a statement.
The EU considers to pay Morocco to fish in occupied Western Sahara. An EU-Morocco Fisheries Agreement from 2013 would be both politically controversial and in violation of international law.
The international Fish Elsewhere! campaign demands the EU to avoid such unethical operations, and go fishing somewhere else. No fishing in Western Sahara should take place until the conflict is solved.