Asked on Sunday whether his forces had control of the eastern Ukrainian city, Mr Zelensky said: "It's a pity, it's a tragedy, but for today Bakhmut is only in our hearts."
His office later clarified that he had not said that the city had fallen.
The Wagner Russian paramilitary claimed to have captured the city on Saturday.
In a video its founder Yevgeny Prigozhin - posing with some of his fighters - said that his forces had control of the entire city.
On Sunday, President Vladimir Putin said that Russia had won the battle for Bakhmut, and that all troops who had excelled would get state awards.
But a spokesman for Ukraine's Eastern Operational Command later told the BBC that Ukraine still controlled several buildings in the south-west of Bakhmut, and was preparing for a counterattack.
He said Ukraine's position was "very difficult" because Russia had destroyed all the city's infrastructure, which limited the number of defensive positions.
But Ukrainian forces were flanking Russian troops and "creating all the conditions on the southern and northern flanks to counterattack and push them back", he said.
At a press conference held at the G7 Summit in Hiroshima later on Sunday, Mr Zelensky said Ukraine's military in Bakhmut was "accomplishing a very important mission".
He said he would not share precise details but insisted the city was "not occupied" by Russia "as of today".
"There are no two or three interpretations of those words," he said.
Mr Zelensky had earlier visited Hiroshima's peace museum, and said the pictures of the city in ruins after the atomic bomb was dropped in 1945 reminded him of present-day Bakhmut.
He added that in the future Ukraine would go through "reconstruction and recovery" as has been seen in Hiroshima.
Analysts say that Bakhmut is of little strategic value to Moscow, but its capture would be a symbolic victory for Russia after the longest battle of the war in Ukraine so far.
The two sides have fought over the city since August.
Western officials estimate between 20,000 and 30,000 Russian troops have been killed or wounded in Bakhmut, while Ukraine's military has also paid a heavy price.
- Killed holding off waves of Russians
- Defending the last Ukrainian streets in Bakhmut
Mr Zelensky was asked about Bakhmut at the meeting of G7 nations in Hiroshima, where he has joined key negotiations.
"You have to understand there is nothing. They destroyed everything," he said, adding that there are "a lot of dead Russians".
"Our defenders... they did strong work, and of course we appreciate them for their great job."
Hardly a building remains standing in the city, and nearly its entire population has fled.
Ukraine's hope is that the long-running battle has exhausted Russia's army and supplies.
Mr Zelensky has previously called the city "a fortress" of Ukrainian morale.
Wagner forces have led the attack on the city, and Mr Prigozhin has frequently criticised the Russian defence ministry for not providing his fighters with adequate supplies.
In Saturday's video, Mr Prigozhin said: "No-one can pedantically reproach us for the fact that at least some piece was not taken."
Yevgeny Prigozhin claimed to control Bakhmut in a video flanked by Wagner fighters
He said Wagner troops would pull out of the city later this month to rest and hand control to regular Russian troops.
Explosions could be heard in the background in the video, suggesting fighting continues close to the city, if not inside it.
He has claimed before that his forces had taken Bakhmut, or most of it, only for the battle to continue.
By Samuel Horti
BBC News