Many children are trained to fight while the girls are turned into sex slaves
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The Ugandan army has rescued 149 children who were being held by the northern-based rebel Lord's Resistance Army (LRA).
The army spokesman, Major Shaban Bantariza, told BBC News Online on Tuesday that in the week-long operation 24 rebels were killed while the army lost three soldiers.
"The children were abandoned by the rebels after army units closed in on them in Gulu, Kitgum and Pader districts," said Major Bantariza.
He said that the children were in poor health - many were suffering from malaria and malnutrition and are now being cared for by local humanitarian organisations.
The LRA, based in the southern part of Sudan, northern Uganda and of late in eastern Uganda, have fought the government since 1988.
Thousands of civilians have been killed and more than a million others displaced by the fighting in northern Uganda alone.
Counter accusations
Humanitarian organisations say that about 20,000 children have been abducted by the rebels over the last five years, with many taken into LRA bases in southern Sudan where they trained as child soldiers while the girls are turned into sex slaves.
The Ugandan government blames Sudan for supporting the LRA; Sudan in turn claims that Uganda supports the rebel Sudan People's Liberation Army (SPLA) which operates from southern Sudan.
Uganda's Defence Minister, Amama Mbabazi, and the head of military intelligence, Colonel Noble Mayombo, held talks over the weekend with Sudanese President Omar al-Bashir.
The official Sudan news agency said President Bashir promised that Sudan would honour its agreements with Uganda so as to maintain a strong relationship with its neighbour.
The two countries signed protocols earlier this month in which Sudan extended for another month a deal permitting Ugandan troops to pursue LRA rebels into Sudan.