"We cannot block the water forever," Prime Minister Yingluck Shinawatra told reporters, adding that the government would choose which parts of the city to allow the water through to minimise the impact.
"The longer we block the water the higher it gets," she said. "We need areas that water can be drained through so the water can flow out to the sea."
The government has reinforced the city's floodwalls in an attempt to prevent the floods pouring into the densely populated city from the central plains, which are several metres under water in places.
Inner Bangkok has so far escaped major flooding as the authorities divert water to areas outside the main capital in a bid to prevent the Chao Phraya River bursting its banks and flooding the political and economic heartland.
But efforts to keep the city of 12 million people dry have been complicated by a seasonal high tide.
"Flood waters are coming from every direction and we cannot control them because it's a huge amount of water. We will try to warn people," said Yingluck, a political novice before taking office barely two months ago.
"This problem is very overwhelming. It's a national crisis so I hope to get cooperation from everybody," added the premier.
Three months of heavy monsoon rains have killed 320 people, damaged the homes and livelihoods of millions of people, mostly in northern and central Thailand, and forced tens of thousands to seek refuge in shelters.
Currently, about one-third of the country's provinces are affected.
The opposition are calling on the government to declare a state of emergency to make it easier to control people and stop them damaging dykes to ease the flooding in their own areas.
Bangkok governor Sukhumbhand Paribatra – a Democrat – warned on Wednesday that seven districts in northern and eastern Bangkok were at risk of inundation because of a broken dyke.
He advised residents in those areas to unplug electrical appliances, move belongings to higher ground and study the city's evacuation plan, saying they had 24 hours to prepare for possible flooding.
The authorities have failed to protect a number of major industrial parks from the gushing brown water, which has inundated hundreds of factories, disrupting production of cars, electronics and other goods.
The government says more than half a million people have been left without work.
Bangkok's main airport is still operating as normal and its flood defences have been reinforced.