At least six people have been killed in clashes between longstanding allies South Sudan and Uganda near their shared border, where competing claims over the poorly defined boundary often flare into small-scale fighting.

Elements from the two armies exchanged fire on Monday in South Sudan's Kajo Keji county, killing five South Sudanese (SSPDF) soldiers, South Sudanese officials said.

Ugandan army spokesperson Felix Kulayigye said SSPDF soldiers had strayed into Uganda's West Nile region and refused to leave, leading to the firefight, in which at least one Ugandan soldier died.

Uganda has backed forces loyal to South Sudanese President Salva Kiir for several decades, helping the country fight for independence, which was won in 2011, and during the subsequent civil war.

Kajo-Keji County said in a statement that five SSPDF soldiers had been killed in a surprise attack by Ugandan forces backed by tanks and artillery. South Sudan's army confirmed the skirmish but did not say how many died.

An existing joint border committee will look at ways to find a peaceful resolution to recurrent border-related disputes, SSPDF spokesperson Lul Ruai Koang said in a statement released late on Tuesday.

In March, South Sudan invited Uganda's army to help bolster security in the capital Juba, following a breakdown in the turbulent relationship between Kiir and his rival, First Vice President Riek Machar.