"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 on Friday.
"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.
Their call comes one week after at least 12 sub-Saharan Africans drowned as hundreds tried to reach the Spanish territory of Ceuta by swimming from a beach in neighbouring Morocco.
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 Malmström, 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.
Spanish authorities say the civil guards did use rubber bullets to ward off the migrants but that they fired them in the air and did not target anyone directly, claims contradicted by witness accounts.
"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.
Morocco, under pressure from Spain, has cracked down on the rising influx of sub-Saharan migrants entering the country illegally and heading to its northern shores in a desperate quest to cross the Mediterranean.
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.
In the face of allegations that several had died at the hands of police in 2013, Rabat launched an operation last month to "regularise" the papers of the estimated 25,000 illegal immigrants on its soil, allowing them to remain and work in Morocco.
Rabat says it has already received 10,000 requests.
Government spokesman Mustapha Khlafi hit back at criticism earlier this week from Human Rights Watch, which said security forces "commonly beat, otherwise abuse and sometimes steal" from migrants.
He said Moroccan authorities were ready to investigate allegations of violence against illegal immigrants.