"If there is someone who can accuse the other, it is me who can accuse Sudan," Kiir said at a joint press conference with the Sudanese president.
"Sudan now is the source of weapons that are going to South Sudan and creating problems for us."
Kiir's accusation came on the second day of his two-day visit to Khartoum aimed at resolving thorny issues with Sudan, including mutual allegations of supporting rebels in each other's countries.
Juba has accused Khartoum of aiding Kiir's opponent and former deputy Riek Machar in South Sudan's ongoing civil war, which has killed tens of thousands and uprooted millions since 2013.
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Sudan has regularly accused its neighbour of supporting rebels in its war-torn Darfur, Blue Nile and South Kordofan regions.
Kiir today reiterated accusations that Khartoum aided Machar, who is currently living in exile in South Africa, and fighters loyal to him.
"Those people of Machar who fled from South Sudan have come here. I can give their names right now," said Kiir.