A spokesman for the US embassy told AFP that “an American citizen” had died in the clashes, which also killed 18 others.
“Yesterday we confirmed the name and we confirmed the fact that the person was killed. We are not providing any additional information about the situation,” the spokesman added.
A spokesman for South Sudan’s armed forces said Allen had not been accredited to cover the conflict by authorities in Juba and it was likely he entered the country through Uganda.
A statement from the rebel SPLA-IO forces condemned the fighting that killed Allen as a “monstrous and unnatural act (that) violates international humanitarian law which entitles journalists to all rights and protection during armed conflicts.”
Allen had worked for several outlets including Al Jazeera and Vice News and previously covered the conflict in eastern Ukraine.
South Sudan’s civil war erupted in December 2013 just two years after it obtained independence from Sudan, when President Salva Kiir accused his former deputy Riek Machar of plotting a coup.
Thousands of people have been killed by the violence, which plunged part of the country into famine earlier this year. Some four million have been displaced, according to UN figures.