South Sudan has descended into renewed conflict in recent months due to the collapse of a power-sharing agreement between rival generals, President Salva Kiir and First Vice-President Riek Machar.
MSF said its hospital in Old Fangak in the north of the country had been bombed, destroying its pharmacy and all its medical supplies. A patient and staff member were injured.
"The attack began at around 4:30 am (0130 GMT) when two helicopter gunships first dropped a bomb on the MSF pharmacy, burning it to the ground, then went on to fire on the town of Old Fangak for around 30 minutes," MSF said in a statement.
It said a drone bombed the town's market next to the hospital at around 7 am, leading to at least seven deaths and wounding 20 people.
"The hospital is clearly marked as a hospital. I don't think it was an accident," Mamman Mustapha, MSF's head of mission in South Sudan, told AFP by phone.
"We've been there since 2014, we've shared our coordinates. They know us. And they continued shelling on the civilian population as well," he added.
The hospital is the only one in the county, serving a population of more than 110,000 people in an area with extremely limited access to healthcare.
It has not been an area at the centre of renewed clashes between the forces of Kiir and Machar in recent months.
But the attack came a day after the Kiir-aligned army chief, Paul Majok Nang, threatened attacks in Fangak and Leer counties in response to a number of boats and barges being "hijacked".
An army statement on Friday accused members of Machar's forces and its allies in the so-called White Army, a militia drawn from the vice president's ethnic Nuer community, of being behind the hijackings, which led to passengers and crew being "held hostage" and ransoms demanded.
A spokesman for Machar's forces described the hijacking claims as "false" and called on the international community to investigate Saturday's assault.
- 'Considered hostile' -
Biel Boutros Biel, a local official in Fangak County, confirmed that bombings had hit the area around 4 am on Saturday.
In a recorded statement, he said they were carried out by a drone and plane, displacing "over 30,000 people" and said a nine-month-old boy was among those killed.
"These planes belonged to the government of South Sudan," he said.
Last week, an opposition lawmaker accused Kiir's government of preparing a "genocide" of the Nuer community after it classified nine out of 16 Nuer-majority counties as "hostile", meaning aligned with Machar's party.
South Sudan has been plagued by instability since gaining independence from Sudan in 2011.
Kiir and Machar represent the two largest ethnic groups, the Dinka and Nuer, respectively.
They fought a civil war between 2013 and 2018 that cost some 400,000 lives.
An MSF hospital was also looted by gunmen in Ulang county, Upper Nile state last month.
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