Around 100 reptiles are thought to be on the loose after escaping from farms in the area and authorities have issued a B1,000 bounty for each crocodile caught alive, said Public Health Minister Vitthaya Buranasiri.
"The crocodiles need to be captured to keep people safe," he said.
The creatures have been spotted in several areas of the former Thai capital, a World Heritage site and major tourist attraction.
Thailand's worst floods in decades have inundated huge swathes of the kingdom, swallowing homes and businesses, shutting down industry, and forcing tens of thousands of people to seek refuge in shelters.
About 300 people have died in the disaster, although there have been no known incidents of animal-related deaths resulting from the flooding.
The natural resource ministry has dedicated a hotline for people wanting to report wild animals on the loose in flooded areas.
"We are now coordinating with the fishery department for a hotline about any loose animals in the flood areas, whether it is tigers, snakes or crocodiles," said an official, who said the department has received "many phone calls".
The ministry said government agencies have been dispatched to catch the creatures, but was unable to disclose how many had been caught. The hotline number inside Thailand is 1362.