Zabihullah Mujahid said urgent aid was being rushed to the disaster zone in the Jalrez district of Maidan Wardak province.
"With great sadness we have received the news that 12 of our compatriots have been martyred and 40 others are missing," he said in a statement.
"Some financial losses have also been incurred."
Although Afghanistan lies on the western edge of the Asian monsoon footprint, flash floods happen regularly during the wet season as heavy rain courses down dry riverbeds.
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