The station serves nearly 400,000 people daily.
A top South Sudan Broadcasting Corporation (SSBC) official, Magok Chilim, said the BBC had ignored requests to “pay arrears”, despite a reminder in January.
He threatened to sue the BBC should the broadcaster not pay its bill.
In a statement, the BBC said it regretted SSBC’s decision to stop broadcasting "its news services to an audience of more than 400,000 in South Sudan”.
The corporation was working hard to reach an accommodation with SSBC to restore the service, it added.
Content courtesy BBC