Forces loyal to Vice-President Riek Machar say government troops attacked their positions in the capital, Juba.
But Information Minister Michael Makuei Lueth said “the situation is normal and it is under full control”.
The UN mission said its buildings had suffered damage, and that hundreds had sought shelter in its compounds.
Col William Gatjiath, Mr Machar’s military spokesman, told the BBC President Salva Kiir “isn’t serious” about a peace agreement.
He said “hundreds” of Mr Machar’s troops had died on Sunday, and that troops loyal to Mr Machar were advancing on Juba from different directions.
Mr Lueth said government troops responded when Mr Machar’s forces attacked a checkpoint, adding that those forces had now been scattered.
The clashes follow days of fighting in the world’s newest country between supporters of Mr Kiir and Mr Machar.
At least 150 people were killed in fighting on Friday, before calm was restored on Saturday. Local radio station Radio Tamazuj reported on Sunday that the death toll from those clashes may be as high as 271.
Heavy gunfire was reported on Sunday near a military barracks occupied by troops loyal to Mr Machar.
Friday’s exchanges were apparently sparked by a shootout between Mr Kiir’s and Mr Machar’s bodyguards. The two men met at the presidential palace on Friday, and issued a call for calm.