Heavy rain followed by flash floods on Friday evening hit the region located on the shores of the lake, damaging dozens of houses, a church, a school and a hotel, BNPB said in a statement on late Saturday.
Lake Toba, the world's biggest volcanic lake, is a popular tourist destination for Indonesians and international visitors.
The flash floods dragged large stones, trees and mud down hillsides, leaving some houses buried to the roof, pictures from the agency showed.
Around 350 people using heavy equipment were carrying out search and rescue efforts, while about 200 people had been evacuated, the agency said.
(Reporting by Bernadette Christina; Editing by Lincoln Feast)