Ministry spokeswoman Candelaria Cedallos said 339 would-be immigrants, mostly male and from sub-Saharan African countries, arrived in five boats between midnight and 10 a.m.
Two of the boats were carrying 103 people each, she said. The migrants included 30 children.
Between Thursday and Sunday, authorities intercepted 476 migrants headed toward the seven-island archipelago located off the northwest coast of Africa.
Officials blamed the latest influx on the fact that the European Union's external borders agency Frontex has yet to resume its maritime vigilance of the area between the islands and the west coast of Africa.
Last year more than 30,000 immigrants were caught trying to reach the Canaries.
Normally, migrants who manage to reach the islands are kept in a holding camp for 40 days and eventually set free, but without residency papers or work permits, if the Spanish authorities cannot identify them.