"The mandate of the United Nations in South Sudan is to supplement, is to support the government of South Sudan, it is not to cause a havoc," government spokesman Ateny Wek Ateny told reporters.
He said the UN's outspoken aid coordinator Toby Lanzer had crossed the line.
"He has made a statement which is not responsible and completely against the government. Toby Lanzer's statement was not giving hope to the people of South Sudan given that he was predicting the total collapse" of the country that is wracked by civil war, he added.
"The president has a prerogative to overturn it. He has not yet overturned it but it is not impossible," he added.
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South Sudan is among the UN's worst humanitarian crises, with more than 2.5 million people facing severe food shortages.
The world's newest state was plunged into conflict nearly 18 months ago between forces loyal to Kiir and rebels allied with his former deputy, Riek Machar.
Lanzer has put the blame for the worsening violence squarely on the shoulders of the leaders who have signed several peace accords and failed to implement them.
Lanzer's expulsion came just weeks before he was to leave for a new assignment.