Lieutenant-General Thomas Cirillo Swaka, then deputy chief of general staff for logistics, resigned last week accusing Kiir, aides and other army officers of violating a 2015 peace deal.
They had "systematically frustrated the implementation" of the peace agreement and sought to "pursue the agenda" of ... the Dinka ethnic community, Cirillo claimed.
But a statement from the army sent to AFP said it was Cirillo who was guilty of misconduct and that it "strongly disputes all inaccurate and inconsistent reasons" he cited for quitting.
"His resignation was aimed at avoiding accountability and escaping justice after a massive corruption was unearthed at his directorate," said a spokesman for the SPLA national army.
Last December, a probe of 51 officers suspected of corruption indicated that Cirillo was "personally and deeply involved in a scam" where huge consignments of military food, fuel and equipment were diverted for "personal use or consumption, disappeared, sold or stolen" it added.
South Sudan gained independence in 2011 but plunged into war in December 2013, pitting the Dinkas of President Kiir against a former vice-president and his Nuer tribe supporters.
Observers said the war later metastasised with other tribes joining one side or the other, often with the hope of getting an upper hand in local conflicts over land and other issues.
An August 2015 peace deal was left in tatters when fighting broke out in Juba in July, with violence spreading throughout the country and no prospects for peace in sight.
In his resignation letter, Cirillo accused Kiir and his entourage of turning the country's military into a Dinka "tribal" army that has taken part "in systematic killings of people, rape of women and the burning of villages in the name of pursuing rebels in peaceful villages".
However in its statement hitting back at Cirillo, whose whereabouts are unknown, the army said he had fled because of the corruption probe.
"His resignation was out of fear that he would be arrested in connection of logistics malpractice. The SPLA challenges him to return to the country so that he clears his name," it added.
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