Recent fighting has raised fears over stability in the run up to the vote, scheduled for January 2011, on whether the south should split away and form a separate country.
The southern army (SPLA) said the militia fighters were loyal to Lam Akol, a southern opposition leader, and accused them of launching a raid on river boats in the Upper Nile state last month.The army raid took place on Friday, it said.
Akol, Sudan's former foreign minister before he formed a breakaway party in the south, was not immediately available for comment. He has regularly denied leading a militia in the past.
Sudan's south has been plagued by a series of uprisings by at least three renegade militia leaders angry at the results of April elections, which saw an overwhelming victory for the region's Sudan People Liberation Movement (SPLM).
So far the skirmishes have not coalesced into a full revolt.
The referendum was originally promised in a 2005 peace deal that ended decades of civil war with north Sudan.
Army spokesman Kuol Diem Kuol said youths led an SPLA division to two hideouts used by a militia loyal to Akol's SPLM- DC (Democratic Change) party in Upper Nile on Friday morning.
"The attacks were really a surprise to them. The SPLA destroyed the two camps. From the side of SPLM-DC seven were killed ... Our forces are now following the remnants and are determined to bring them to justice," he said.
Four SPLA soldiers and many militia fighters were injured in the clash, he added.
