Valencia said they were "deeply saddened by the passing of Fernando Martin, coach of Valencia CF Femenino B, and three of his children, in the tragic boat accident in Indonesia, as confirmed by local authorities".
Indonesian and Spanish authorities said on Saturday that Martin and three of his children were missing after the boat carrying 11 people sank in extreme weather on Friday in the Padar Island Strait near the island of Labuan Bajo, a popular tourist spot.
The search was continuing on Sunday morning, Fathur Rahman, mission coordinator for Indonesia's search and rescue agency in the area, told Reuters.
Real Madrid CF also sent condolences for Martin, 44, a former player in second-tier Spanish football who was appointed coach of the Valencia Women's B team this year.
His wife and one daughter, as well as four crew members and a tour guide, were rescued and safe, SAR said in a statement.