The governor, however, said due to improvement in efficiency BMA officials managed to tackle flooding in most areas before the morning rush hours at 7am.
He said flooding on Sukhumvit Soi 26 was resolved by 8.30am as the area was complicated.
"I've instructed BMA officials to make preparations to deal with flooding during the rainy season since early this year by draining sewers and increasing the capacity of our water pumps," the governor posted on his Facebook wall.
The flooding monitoring centre of the BMA's Drainage and Sewerage Department reported that it had tackled waterlogging at several spots in the capital.
It said it took about one hour to drain floodwater under the BTS Baring station after the area was flood at 1.30am.
It also took about an hour to drain floodwater in front of the Benz showroom on Pattanakarn Road in Suan Luang district after flooding was reported at 1.45am.