The human rights organization accused Spain of carrying out unlawful deportations to Morocco and the unnecessary or excessive use of force by law enforcement officials at the enclave borders.
"Thousands of migrants, including asylum seekers and refugees, some fleeing from Syria, attempted to irregularly enter the Spanish enclave cities of Ceuta and Melilla from Morocco. Reports of unlawful deportations and excessive use of force by Spanish border guards persisted," read the annual human rights report on 160 countries.
Amnesty highlighted the deaths of 15 migrants last February when Civil Guards used anti-riot gear, including rubber bullets and smoke cannisters, to prevent an attempt by a group of around 250 people to swim across the sea border between Morocco and Ceuta.
A judge last month ordered 15 Civil Guards to be appear in court over the drownings while another 24 officers are facing criminal charges for their treatment of migrants in both enclaves.
The report also said that hundreds of thousands of irregular migrants continued to have access to free health care limited, under a 2012 law that contravenes the European Social Charter.
Spain's treatment of Syrian refugees was also noted in the report.
"Despite the government’s announcement in December 2013 that it would resettle 130 Syrian refugees, by the end of 2014 none had been resettled," read the report which stated that by the end of 2014 more than 1,500 Syrian refugees were waiting to be transferred to the mainland from the enclaves.
The Spanish´s government´s refusal to address crimes of the Spanish Civil war and ensuing 36-year fascist dictatorship of General Francisco Franco also fell under scrutiny.
"The rights to truth, justice and reparation for victims of crimes committed…continued to be denied," the report said.
Spain was also criticized for the "excessive use of force" used by police to disperse and detain protestors and said that freedom of assembly was being eroded.
"Throughout the year, hundreds of individuals were detained and fined for participating in spontaneous and mostly peaceful demonstrations of more than 20 people."
But Spain did win credit for ratifying the UN Arms Trade Treaty last April, and "in August became the first country to update its regulations on arms transfers to include the 'Golden Rule' prohibiting the transfer of arms where there was a real risk that they would contribute to human rights violations," Amnesty International said.