The Water and Flood Management Commission (WFMC) and the BMA are locked in a dispute over the placement of sandbags in the city's drains.
The WFMC said the sandbags disrupt water drainage, while the BMA claimed it is part of the city's flood prevention measures.
Mr Pramote, who discussed flood prevention with City Hall officials yesterday, said the WFMC did not understand the BMA's technique of using sandbags to block the drains.
The WFMC is a national agency and if it interferes too much in the BMA's flood prevention activities, the measures may not make any headway, Mr Pramote said.
The commission must come up with broad strategies and allow other agencies to help implement them, he said.
"But the WFMC's strategies are still vague. It must think more clearly about this [issue]," said Mr Pramote, who earlier questioned WFMC chairman Plodprasop Suraswadi's water management knowledge.
Mr Plodprasop, who is also the Science and Technology Minister, yesterday issued an ultimatum to the BMA to remove all the sandbags stuffed in the city's drains within 15 days.
Mr Plodprasop said he had ordered the secretary of the WFMC to send a letter to the BMA asking City Hall to disclose other locations where it had blocked drains with sandbags other than along Srinakarin Road.
If the BMA fails to comply, the WFMC will send its own men to remove the sandbags, he said.
The BMA's technique of using sandbags to block the drains is not in line with the standard principles of drainage, he said.
The WFMC chairman said the law says clearly that the government has the power to take action for the benefit of the public.
Therefore, he is not worried about the BMA's threat to take its case to the Administrative Court if the sandbags it owns are removed by other agencies.
Bangkok governor Sukhumbhand Paribatra, however, argued that the BMA has the authority to run areas under its jurisdiction according to the BMA Act, and there is no need for City Hall to report the matter to the WFMC.
He insisted the sandbags had not blocked waterflow in the drains and that the technique has long been part of the BMA's flood prevention measures.
"If anyone wants to know the facts, they should ask the BMA, not remove the sandbags like this," MR Sukhumbhand said, referring to Pheu Thai Party spokesman Prompong Nopparit and his deputy Jirayu Huangsap, who lifted sandbags out of a sewer on Srinakarin Road on Sunday as part of their inspection of the BMA's dredging work.
Democrat spokesman Chavanond Intarakomalyasut said the Democrat Party will consider if the Pheu Thai MPs had interfered with the work of government officials, violating Section 266 of the constitution, when they removed the sandbags.