There were no casualties in the strike that hit the newly built clinic in the Abs region, which was empty at the time, said the charity, commonly known by its French initials MSF.
"This morning's attack on an MSF cholera treatment centre by the Saudi and Emirati-led coalition shows complete disrespect for medical facilities and patients," said MSF's head of mission Joao Martins.
"MSF has temporarily frozen its activities in Abs until the safety of its staff and patients is guaranteed," he said.
The charity said the facility's roof clearly identified it as a medical centre and that its coordinates had been given to the coalition.
Saudi Arabia, the United Arab Emirates and other allies intervened in Yemen in 2015 to try to restore the internationally recognised government to power after the Iran-backed Huthi rebels ousted it from swathes of the country including the capital Sanaa.
A spokesperson for the Saudi-led coalition was not immediately available for comment.
Since July 2015 MSF has supported the Abs hospital, just one kilometre away from the cholera treatment centre hit Monday, according to the charity's website.
On August 15, 2016, an airstrike destroyed part of the Abs hospital, killing 19 people -- including an MSF staff member -- and wounding 24 others.
Shortly after the deadly raid, MSF suspended operations in several facilities in the country's north.
But last November, the group returned to Abs after the hospital's reconstruction was complete -- employing about 200 national workers and a dozen international medical professionals since.
In December 2016, the coalition acknowledged that it had targeted the MSF-supported hospital due to an "unintentional mistake".
The conflict has killed nearly 10,000 people and wounded more than 55,000, according to the World Health Organisation.
More than 2,200 people have died of cholera and millions are on the brink of starvation, in what the United Nations has called the world's worst humanitarian crisis.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)