Bangkok Governor Sukhumbhand Paribatra, however, maintains the controversial trial should be postponed.
"I can assure you that there are no conflicts [between us] at all, but only concerns raised," Mr Yongyuth said during a joint press conference with MR Sukhumbhand and his deputy, Teerachon Manomaiphibul, yesterday.
The joint press conference was held after City Hall disagreed with the government's plan to conduct a trial of water drainage systems in Bangkok on Wednesday and Friday.
The plan was initiated by Science and Technology Minister Plodprasop Suraswadi, chairman of the Water and Flood Resources Management Committee (WFRMC).
The Bangkok Metropolitan Administration (BMA) feared the trial would cause floods in some areas.
MR Sukhumbhand said yesterday the Bangkok Metropolitan Administration was not opposed to the WFRMC's plan to test the canal network's drainage capacity in the east and west of Bangkok.
He said his concerns centred on a weather forecast that heavy rain was expected across 60% of Thailand. A storm would probably reach the country next week at the time the drainage test is being carried out, he said.
Khlong Lat Phrao and Khlong Bang Sue - that are under the care of the Science and Technology Ministry - have yet to be dredged properly to make them ready for the test, the Bangkok governor said.
The BMA would order its water gates closed immediately if water in the canals rises to an unusually high level in flood-prone areas including the Sethakij community in Bang Kae district.
BMA officers will be sent to these flood-prone areas to monitor water levels and promptly alert the BMA authorities to consider shutting the water gates.
Unforeseen consequences could erupt if the drainage test coincides with the run-off and high sea levels, Mr Teerachon said.
He said he was not against the drainage trial but would rather that Mr Plodprasop consider postponing it until conditions posed less risk.
Mr Yongyuth said he would then inform Mr Plodprasop about the need to dredge the canals before the drainage test begins.
Mr Plodprasop yesterday said Mr Teerachon was "telling a lie" about high sea levels expected during the drainage test next week as that the information he had showed that next week would have the lowest sea levels of the year.
He insisted that the proposed drainage trial had been well planned in advance.
Mr Plodprasop also argued that the dredging of Khlong Lat Phrao was 50% completed and that the canal was ready to receive water flows during the flood drainage test.
High tide is projected at 2.9 metres above the average sea level between 8pm to 10pm on Wednesday and Friday, an officer at the Royal Thai Navy's Hydrographic Department said, adding that next week is not a high tide period.
Meanwhile, Prime Minister Yingluck Shinawatra yesterday presided over the opening of an exhibition on the government's water management scheme entitled "Working Hard towards Water Management for all People" at Bangkok Convention Hall, Central Plaza Lat Phrao.
The premier led a a group of Thai and foreign media, diplomats and private sectors touring the event, which will run until Sunday, and aims to boost public and foreign investors' confidence about the government's flood prevention scheme.
"The government has brought the experience of last year's floods to improve water management to prepare for possible disasters in the short- and long-term periods," she said.
Payungsak Chartsutthipol, chairman of the Federation of Thai Industries, who participated in the exhibition, said that the private sector would like the government to balance the importance between flood and drought management because they could both cause damage to the country's economy.