Video by Thiti Wannamontha
The death toll from the floods had risen to 31 as of Sunday morning, the department said.
Chanthaburi, Chon Buri and Khon Kaen provinces have recently been hit by flooding, but the situation had eased in Kanchanaburi, Prachuap Khiri Khan, Chumphon, Kalasin, Nakhon Ratchasima, Phayao, Mae Hong Son, Lampang and Mukdahan.
Meanwhile, authorities are speeding drainage in eastern Bangkok as more water has been discharged from the Pasak Jolasid dam in Lop Buri.
Adisak Khantee, director of the Bangkok Metropolitan Administration's Department of Drainage and Sewerage, said on Sunday that the Meteorological Department expected rainfall in 40% of the capital.
But the more worrying issue is the mass of water run-off from the North, as the amount of water in the Pasak Jolasid dam has exceeded its capacity, he said.
The Rama VI dam is receiving water discharged from the Pasak Jolasid dam at the rate of 859 cubic metres per second and some of the water will enter eastern Bangkok, he said.
Mr Adisak said the BMA is draining water out of canals in preparation for the run-off.
In Sa Kaeo, many main highways have been flooded and are impassable to any kind of road vehicle.
Pol Sub Lt Wisal Juengtrakul, a highway police officer, said a huge volume of run-off water from Khao Soi Dao mountains in Soi Dao district of Chanthaburi province has inundated much of Wang Sombun, Wang Nam Yen, Khao Chakan and Muang districts of Sakaeo.
A 700-metre section of Highway 317 (Chanthaburi-Sakaeo) at Ban Khao Laem in Wang Sombun district was under one metre of water on Sunday afternoon.
A section of the Aranyaprathet-Khao Hin Son road was also one metre under water at Ban Sa Khwan in Muang district.
Highway 33 (Sakaeo-Kabin Buri) was under 80cm of water, blocking all of its four lanes.
Sakaeo has virtually been cut off. It has become inaccessible from Prachin Buri's Kabin Buri district and Chachoengsao's Phanom Sarakham district.
Highway police were looking for routes which could be used to reach Sakaeo, Pol Sub Lt Wisal said.