"Our conscience is clear, and Morocco will continue to be completely transparent on these issues," Salaheddine Mezouar told reporters in a joint press conference in Barcelona with his Spanish counterpart.
Rabat "will defend itself with the law and the truth", he added.
The statement comes after a Spanish judge last Thursday upheld charges against 11 Moroccan ex-security officials and governors accused of taking part in ethnically-motivated torture, killings and detentions in the disputed former Spanish colony between 1975 and 1991.
Victims cited in the ruling claimed they were beaten, burnt, electrocuted and sexually assaulted while held by Moroccan security forces. Relatives of others said their loved ones simply disappeared.
In Barcelona, Mezouar said "all victims of political violence were compensated in 2004".
Describing Spain as a "strong strategic partner" of Morocco, he added:
"Many people are trying to create difficulties to undermine relations between the two countries."
The Moroccan government expressed "astonishment" over the judge's decision in a statement on Saturday.
Judge Pablo Ruz's ruling came a day before the UN Security Council received a report from UN chief Ban Ki-moon calling on Morocco and Western Sahara's pro-independence Polisario Front to enter talks brokered by the UN envoy to the region.
The Moroccan and Spanish ministers met as representatives from Europe, the Middle East and North Africa gathered in Barcelona for a meeting of countries located on the Mediterranean.
Morocco took control of most of Western Sahara in November 1975 after Spain withdrew and fought a 16-year conflict against the pro-independence Polisario Front.
Repeated bids by UN mediators to organise a referendum on self-determination for Western Sahara have since failed.