Colonel Khalid Ono Loki is the second top army official to quit this week after a respected general resigned while accusing President Salva Kiir and top members from his majority Dinka tribe of "ethnic cleansing".
The country's labour minister also resigned yesterday, and declared allegiance to rebel leader Riek Machar. The exodus comes amid mounting alarm over a civil war which has devastated the world's youngest nation over the past three years.
In a letter addressed to army chief Paul Malong Awan, Loki decried "unspecified and unstipulated arrests and detentions fluctuating from months to years without investigation and scrutiny ... On fabricated cases against individuals of non-Dinka ethnicity."
"Mr. Chief, you have often avoided the current courts, tried officers on your own, whilst crafting and forming alien ones paradoxical to the existent established courts which are in conformity with the law," Loki wrote.
"Your unqualified clique of friends and relatives who dangerously arrest and sentence as you so wish and command have never attended any law school to carry such responsibility."
War broke out in oil-rich South Sudan in 2013, just two years after it achieved independence, after Kiir accused his former deputy Machar of plotting a coup.
Violence -- initially between ethnic Dinka supporters of Kiir and ethnic Nuer supporters of Machar -- has since spread to other parts of the country, engulfing other ethnic groups and grievances.
The United Nations has warned of potential genocide and ethnic cleansing.
A confidential UN report obtained by AFP this week cites UN Secretary-General Antonio Guterres as saying the war had reached "catastrophic proportions for civilians".
Rights groups accuse both soldiers and rebels of horrific rights abuses including rape and extra-judicial killings.
The humanitarian crisis has been exacerbated by a severe drought which has put thousands at risk of famine in the country.
The UN's humanitarian office OCHA said some 7.5 million people in the country were now in need of humanitarian assistance.
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