Prime Minister Prayut Chan-o-cha has refused to use his special powers to take action against Bangkok governor MR Sukhumbhand Paribatra over his failure to contain serious flooding earlier this week.
The premier suggested Bangkok residents make their own decision at the next governor election.
The move follows City Hall's failure to prevent flash flooding in the capital caused by torrential downpours on Monday and Tuesday mornings while MR Sukhumbhand was on an overseas trip to the Netherlands.
However, City Hall blamed mountains of garbage being dumped at a rate of 1,000 tonnes a day and which were blocking waterways as being the main cause of the floods.
The Stop Global Warming Association has called on the prime minister to invoke Section 44 of the interim constitution and sack the governor, alleging he has proved himself to be incompetent in handling the capital's flood management.
ฺBut Gen Prayut on Tuesday brushed aside calls for him to exercise Section 44, saying he could not do so because the Bangkok governor was an elected official voted into office through an election.
Instead, Gen Prayut said Bangkok residents should make up their own minds and monitor the work of the Bangkok governor. They can make their decision at the governor election due in 2017, he said.
However, Gen Prayut said that if City Hall makes little progress in solving the flood issue, he will instruct the permanent interior secretary, who oversees City Hall, to tackle the problem.
"People must monitor [the governor's work] as they elected him. Did you elect him? How can you simply want me to use that power," Gen Prayut said.
Gen Prayut said he will ensure fairness for all sides, adding that authorities must come up with measures to tackle the causes of flooding, such as rubbish clogging the drainage system.
"It [City Hall] has to examine why the flooding happened, firstly heavy rainfall of as much as 140 millimetres, and secondly whether plans were prepared," Gen Prayut said.
"I heard that among four key water pumps, only one was being operated. Why? There was a report that a mattress was put inside the pump. Where did it come from? We need to be fair to City Hall as well."
The prime minister said he had set up a military unit for rapid deployment to deal with flash foods in the capital's flood-prone areas.
MR Sukhumbhand has been targeted for criticism since Monday morning, when five hours of torrential downpours in the early hours left many areas of the capital heavily inundated.
Frustrated commuters and children were stuck in traffic gridlock on their way to work and school along flooded roads.
Many schools and offices in the city declared an impromptu holiday on Monday.
Heavy rain also hit some areas in the capital Tuesday but did not cause the same degree of havoc.
Wasant Meewong, MR Sukhumbhand's spokesman and adviser, came out to defend the governor on his Facebook page.
"MR Sukhumbhand has never dodged a problem, not even once. But he lets his actions, not his words, speak for themselves," Mr Wasant wrote.
He challenged the Stop Global Warming Association and its leader Srisuwan Janya to show what they have actually achieved, besides putting themselves in the public spotlight.
Mr Wasant said city workers tried diligently to drain off the flood water, insisting that City Hall was more efficient in draining off the flood water in just two to three hours instead of a few days as happened during the floods four years ago.
A source at City Hall said MR Sukhumbhand has decided to cut short his visit to the Netherlands and would return to Bangkok Wednesday out of concern over the flood situation.
The governor has been attending the 2nd Policing in Global Cities international meeting in Rotterdam, scheduled to run from last Saturday to Friday to take part in discussions on measures to prevent flooding and cope with climate change.
City Clerk Sanya Chenimit said Tuesday that rubbish clogging the drainage system was a major problem.
He said at least 1,000 tonnes of waste were collected from the sewerage systems and canals each day although there are not enough city workers to collect it all.
The amount collected is much higher during the rainy season.
Mr Sanya urged the city's residents not to litter the streets and canals.