"Our troops have entered Mahagi town and we are in control," Uganda's defence and military affairs spokesman Felix Kulayigye told AFP Sunday.
The deployment was requested by the Congolese army following alleged massacres of civilians carried out by a militia known as the Cooperative for the Development of Congo (Codeco), he said, without providing further details.
Mahagi is in Ituri province, which borders Uganda, where at least 51 people were killed on February 10 by armed men affiliated with Codeco, according to humanitarian and local sources.
Codeco claims it defends the interests of the Lendu community, mainly composed of farmers, against the Hema community, mainly herders.
Uganda already has thousands of troops in other parts of Ituri under an agreement with the Congolese government.
Last month, Uganda announced its troops had "taken control" of the provincial capital, Bunia.
Ituri is just north of the provinces of North and South Kivu, which at the end of January fell under the control of the anti-government M23 armed group, which is backed by neighbouring Rwanda.
Analysts fear that Uganda and Rwanda's growing presence in eastern DRC could lead to a repeat of the so-called Second Congo War, which lasted from 1998 to 2003, involving many African countries and resulting in millions of deaths from violence, disease and famine.
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