Local people had hoped that all the floodwater would be cleared by Friday but the opposite occurred.
"Yasir Niamatullah, chief of Hyderabad module, and Athaullah Rehman, a motivator who raised funds, have been arrested by the NIA.
The judge remanded them in judicial custody though the investigating agency has filed an application seeking their police custody for further examination.
In its application, the investigating agency stated that the accused need to be taken to Maharashtra and Rajasthan and it also wanted to question them on the possibility of recovering more explosives.