"Spain deeply regrets this and is sorry that it happened. We offer our apology and consider the matter closed," Spain's Ambassador to La Paz Miguel Angel Vasquez said after delivering a written note to the Foreign Ministry.
Bolivia has joined Venezuela and Nicaragua in offering asylum to Edward Snowden, the former IT contractor for the US National Security Agency who publicized details of US surveillance programs and is now on the run from espionage charges.
Earlier this month, during a flight home from Moscow, European authorities diverted Morales's plane to Austria and searched it after rumors he had Snowden on board.
Venezuelan Foreign Minister Elias Jaua called the incident "an attack against President Morales's life," echoing earlier claims by Bolivia itself.
Brazilian President Dilma Rousseff expressed "indignation" over the treatment of Morales, calling it a "provocation" that concerned "all of Latin America."