The human rights organisation says security forces from both countries violated the basic rights of undocumented immigrants attempting to enter the Spanish enclaves of Ceuta and Melilla, which constitute Europe's only land borders with Africa.
In a report released in Madrid on the eve of a European Union summit due to discuss immigration, Amnesty also accused the EU of contributing to a chaotic situation and focusing on "keeping people out of Europe".
It said at least 11 people had been killed and many others injured while trying to enter the Spanish outposts on Morocco's Mediterranean coast.
Police used "unlawful and disproportionate force" including lethal weapons against people trying to scale the border fences, said Javier Zuniga of Amnesty's delegation to Spain and Morocco.
"Many of those seriously injured inside Spanish territory were pushed back through fence doors without any legal formality or medical assistance," he added.
Without food and water
In addition, Morocco had left hundreds of migrants in remote desert regions bordering Algeria with no or inadequate supplies of food and water, according to the findings.
Amnesty said Morocco used repressive methods even against asylum seekers and people already recognized as refugees by the United Nations High Commissioner for Refugees (UNHCR).
"Many of those seriously injured inside Spanish territory were pushed back through fence doors without any legal formality or medical assistance"
Amnesty's delegation to Spain and Morocco
It called for a "global strategy that ensures that the human rights of some of the world's poorest people are protected".
The Spanish daily El Pais, meanwhile, said the UNHCR had been unable to clarify the fates of 85 refugees or asylum seekers detained by Morocco while attempting to reach Ceuta or Melilla.