Alfredo Perez Rubalcaba said a Spanish fishing vessel made the discovery Wednesday night off the coast of West Africa, and a survivor from the migrant boat said 50 people were missing.
The ship's skipper, Jose Maria Abreu, told Cadena Ser radio he counted seven dead on the boat, and that the survivor was in deplorable physical condition.
"The stench was unbearable. They must have been dead six or seven days," Abreu told the radio station.
Rubalcaba told a news conference the number of people caught this year trying to sail from Africa to Spain, either to the mainland or the Canary Islands, is down sharply to 13,000 from 35,000 last year.
Perez Rubalcaba attributed the drop to a new European surveillance system with aircraft and ships posted off the coast of Africa. He said this is discouraging people from setting out on dangerous journeys to Spain, which for destitute Africans is seen as a gateway to a better life in Europe.