The natural disaster took place on Friday night in Cilacap district of the province, an official in charge of the national disaster management agency said.
"The damages and casualty were caused by whirlwind. Currently one person was recorded dead and the number of houses destroyed was 161 units," the official told Xinhua.
Risks assessment of the disaster is being carried out by local authorities, the disaster has forced scores of people to flee home and take shelters in their neighbor's or relatives' houses, the official said.
Whirlwind has frequently stricken across the archipelagic nation, leaving damage and casualties.