The country seceded from Sudan a year ago under and is awash with weapons after a decades-long civil war with Khartoum that killed an estimated two million people.
The government, run mostly by former guerrilla fighters, has struggled to assert control over its vast and restive territories since declaring independence.
A group led by rebel leader David Yau Yau - one of several militias fighting the government - attacked the convoy of 200 soldiers near Pibor, a remote corner of the eastern state on Jonglei, army spokesman Philip Aguer said.
Twelve soldiers were wounded in the attack on Wednesday and 17 are missing, he said.
The troops had been sent to investigate reports that Yau Yau had been sighted in the area, Aguer said.
He said he suspected the rebels were joined by youth from the Murle tribe who are resisting government efforts to give up their weapons.
Nearly 900 people died when about 7,000 armed youth of the Lou Nuer tribe attacked Murle villages in the Pibor area at the end of last year, according to the United Nations.
Last week Human Rights Watch issued a report saying soldiers had raped, beaten and killed civilians during the disarmament campaign, allegations denied by the government.
South Sudan voted overwhelmingly for independence from Sudan in a 2011 referendum promised under a 2005 peace deal that ended the civil war.
The two countries are still negotiating issues including border security and disputed territories, and the two armies have clashed in border states since secession.