She made the call during a virtual cabinet meeting on Monday, Cabinet Secretary Khandker Anwarul Islam said.
"Discussions at the meeting largely focused on the floods and rehabilitation efforts. Flood waters have been receding over the last few days. The waters of the Jamuna River near the Bangabandhu Bridge have already dropped below the danger level."
The water level and currents in the Padma River are also declining but the Indian Met Office predicts there could be more rains in the upstream, Anwarul added.
"The prime minister particularly warned about this possibility and instructed the authorities to be prepared for long-term floods."
The ongoing floods have inundated nearly a quarter of the country this year. As many as 161 people have lost their lives, mostly from drowning, according to government data.
Although the water level has started falling gradually in the Brahmaputra-Jamuna and Ganga-Padma basins, the northeast and southeast regions may experience flooding again by the end of the month due to heavy monsoon rains, the Met Office warned.