Some members of M23, a Tutsi-led rebel group that once controlled vast territory in eastern Congo, "have been quietly escaping into the general public," government spokesman Ofwono Opondo said in a statement.
Opondo said Ugandan authorities have arrested 101 M23 members, disguised as ordinary passengers, who were being ferried in four vehicles destined for Congo.
"Uganda will not and does not support any armed activities to destabilise the Democratic Republic of Congo," he said.
It was not clear if M23 leader Sultani Makenga remained in the custody of Ugandan authorities. Makenga is the subject of US sanctions, including a travel ban and assets freeze for "serious violations of international law involving the targeting of women and children" in armed conflict.
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The news of missing M23 fighters is likely to alarm Congo's government, which has repeatedly urged Uganda's government to hold the rebels.
M23 launched its rebellion in eastern Congo in April 2012, becoming the latest reincarnation of a Tutsi rebel group dissatisfied with Congo's government, until it was repulsed by UN forces and Congo's army. Many rebels fled to Rwanda and Uganda before a 2013 peace agreement.