The move has fueled speculation that Martin, who came out in 2009, plans to marry his partner Carlos Gonzalez Abella.
Spokesman Jose Blanco told a news conference that ministers had agreed to grant him a “letter of naturalization”, issued in special circumstances, because of his “personal and professional links with Spain.”
Spanish newspaper El Pais reported that Martin sought citizenship in order to marry boyfriend Carlos Gonzalez Abella, with whom he is bringing up his twin three-year-old sons.
Spain passed legislation allowing same-sex marriages in 2005, only the third country to do so at the time, with 20,000 gay couples entering into marriage since.
Martin has previously suggested he wanted to get married, saying: “I would get married… There are many countries around the world where same-sex marriage is a right. Not in Puerto Rico, unfortunately. And not in many states in America.”
El Pais reported that Martin was not asked to renounce his Puerto Rican or U.S. citizenship.