"We are deeply concerned to see the close cooperation between Spain and Morocco on border control today resulting in... Widespread violence against migrants and security practices outside of any legal framework," the eight NGOs said in the open letter seen by AFP today.
"We ask you to intervene urgently with your government to put an end to these practices," said the group, with included the Moroccan branch of Caritas and migrant support group GADEM.
The incident has fuelled international concerns about the violent treatment of illegal immigrants by Spanish and Moroccan security forces amid reports that Spain's civil guards fired rubber-coated bullets at those attempting the crossing on February 6.
The European Commissioner for Home Affairs, Cecilia Malmstrom, said on Friday that she was "very concerned" about Spanish border police using rubber bullets to deter migrants, and expected "clarifications," in a comment posted on Twitter.
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"Last Friday, we received several dozen people who were part of the group that tried to enter Ceuta on the morning of February 6," the letter by the Moroccan NGOs said.
"Those who went by sea witnessed Spanish security forces firing rubber bullets and tear gas at the boats and the people themselves, even as they were calling for help."
The letter to the ambassador argued that the Spanish government had "responsibility" for the growing number of human rights violations against migrants either side of its North African borders.
Ceuta and Melilla, Spain's other enclave bordering Morocco, have the EU's only land borders with Africa and are seen as stepping stones to mainland Europe.