The Hanoi Sewerage and Drainage Company said it was heavy rain rather than its opening of the West Lake floodgate that flooded the river.
The Japanese had complained that the flooding had wiped out all the microorganisms they had been using to clean the river, forcing them to start over.
According to a statement issued by the Hanoi company earlier, the floodgate's opening on July 9 was to maintain the lake's level and flush the To Lich River.
Vo Tien Hung, general director of the utility, said Tuesday the Japan-Vietnam Environmental Improvement JSC (JVE), which is in charge of the cleanup, had been notified prior to opening the floodgate but made no response.
He also said his company had discharged water "very slowly" over two days to make sure it did not flood JVE's testing area, which was only flooded because of heavy rain on July 15.
Hung said the his company is not a competitor in treating the To Lich River, and thus has no movitation to sabotage the Japanese team's work.
Le Tu Luc, deputy chief of staff of the Hanoi's People's Committee, said that the Japanese team had been notified, before they started the cleanup, that the To Lich had a constant flow and was the main drainage for the city during rains.
At a meeting on Monday, Hanoi officials said that the Japanese team only had one week to prepare for the cleanup project, which was not enough for them to conduct detailed surveys or fully gather information about natural conditions, the weather and the To Lich's water level and flow speed, Luc said.
It had also failed to refer to the operation manual for the city drainage system, he said.
The discharge of water from the West Lake into the river was in fact a regular operation to prevent flooding, he explained.
The trial cleanup of a section of the river using nano-bioreactor technology began in May and was scheduled to finish on July 17.
The Japanese side has however requested that the date be pushed back to September 17 following the setback.
The nano-bioreactor technology works by infusing oxygen into the river to activate beneficial microorganisms and create an environment for them to live in.
The To Lich used to be a branch of the Red River but was delinked by the French in 1889 as part of an urban plan.
Over 200 sewage outlets empty 150,000 cubic meters of untreated household wastewater every day into it, according to the city Department of Natural Resources and Environment.
Wastewater from factories adds to the pollution.
The river runs 14 kilometers (8.7 miles) through the downtown districts of Thanh Xuan, Hoang Mai and Thanh Tri.
Hanoi has tried in vain to clean it many times in the last decade.