Zabihullah Mujahid said the scale of the damage had been worse because of the mismanagement of infrastructure by the previous government.
However, the hardline Taliban regime that returned to power a year ago is also struggling to cope.
"If the floods and the losses increase, the Islamic Emirate of Afghanistan does not have that many resources to respond to all of it," Mujahid told a press conference in Kabul.
Heavy rains have lashed several provinces, with the worst of the flooding in the east of the country.
Dozens of Afghans die every year in torrential rains -- especially in poor rural areas where badly constructed houses can easily collapse.
Since the Taliban took control of Afghanistan the country has been plunged further into economic and humanitarian crises, worsened by the freezing of billions in assets held abroad and a slash in aid funding.
The Taliban called on the international community, particularly Muslim countries, to help the government meet the needs of flood victims.
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