Lieutenant-General Thomas Cirillo Swaka was the country's deputy chief of general staff for logistics and a respected figure among the country's foreign partners.
I "have lost patience with the conduct of the president and commander in chief, the chief of staff and other senior officers in the headquarters of the SPLA as well as unit commanders," Cirillo wrote.
Kiir and other officers of the SPLA -- the country's national army -- "have systematically frustrated the implementation" of a 2015 peace agreement and sought to "pursue the agenda" of the elders' council of the Dinka ethnic community, Cirillo charged.
Concurring sources later told AFP that Cirillo had now left the country, but were unable to say where he had gone.
South Sudan gained independence in 2011, but broke out into war in December 2013, pitting the Dinkas of President Kiir against former vice-president Riek Machar and his Nuer tribe supporters.
Observers said it 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.
Tens of thousands have died in the conflict, despite a 12,000-man UN peacekeeping force posted in the area, while over three million have been displaced.
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".
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