In Galicia, an autonomous community in northwest Spain, the conservative Popular Party won 41 of the 75 seats in the regional Parliament, near-complete results of Sunday elections indicated.
This marked a gain of three seats over the Spanish Socialist Workers Party and two smaller rivals.
In the Basque region, the Basque Nationalist Party -- known regionally as the Basque Party of Supporters of God and Old Laws -- won the largest bloc of seats, 27 out of 75, while the more radical separatist Euskal Herria Bildu political coalition came in second with 21, the results indicated.
This gives separatists 48 of 75 votes in the regional Parliament.
The Popular Party and the incumbent Spanish Socialist Workers Party fell to 26 combined seats in the 75-seat Basque Parliament from 38, the available returns showed.
The elections were widely seen as a referendum on Rajoy's management of Spain's debt crisis and his program of economic-austerity measures to resolve it in the face of popular protests.
The Galicia results will likely give Rajoy leeway to carry out austerity measures, the Spanish newspaper El Pais said.
The Basque separatist victory, weeks after a mass rally for independence in Catalonia, sends an "unequivocal message" that could further strain relations between Madrid and some of Spain's 17 autonomous regions, the newspaper said.