The attack took place at 0930 hrs local time in Jonglei near Gumruk, Army sources said here.
A Lt Colonel and a Junior Commissioned Officer (JCO) were among those killed in the incident, they said.
"Peacekeepers from India in UN Mission in the Republic of South Sudan (UNMISS) attacked in Jonglei," an MEA spokesperson said here.
Arrangements are being made to bring back the bodies of the Indian peacekeepers.
Last month, an Indian soldier was shot there amid fears of a government crackdown.
India is a major contributor to UN peacekeeping forces around the world and has suffered losses in the past.