"We will equally hold accountable those who got engaged in targeting, killing, trying to use the ethnic card, definitely within the organised forces," Barnaba Marial Benjamin told reporters during a visit to London.
"A good number of officers have been arrested -- about 100 who were engaged in this -- of the Dinka members within the army who targeted the Nuer community (of former vice-president Riek Machar). They will be held accountable."
Thousands of people have been killed in South Sudan in the last two months in fighting pitting soldiers loyal to President Kiir against a loose coalition of army defectors and ethnic militia nominally led by Machar.
Many fear the conflict has slid out of the control of political leaders, with ethnic violence and revenge attacks between the Dinka people of Kiir and the Nuer of Machar, the country's two largest groups.
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"There is a Dinka-Nuer ethnic sort of fight," Benjamin acknowledged, but said it was "in a limited zone, it is within the national army as well as the rebel army. It is not among the citizens".
The minister said his government was "completely determined and committed" to the January 23 ceasefire, which has been repeatedly violated.
Benjamin said that four political prisoners held in Juba since mid-December, a source of contention between the two sides, would stay behind bars until the necessary "legal processes" were complete.
If they are found guilty, he said, "it will be up to the president because our constitution gives the prerogative to the president where he can sometimes issue pardons".
At their meeting, Simmonds stressed that the new round of peace talks taking place in Ethiopia this week "must be inclusive, and have a role for those political leaders who were detained at the start of the conflict".