Sultani Makenga is said to have handed himself over along with hundreds of M23 fighters in the Mgahinga National Park.
Neither government has so far confirmed the reports.
Earlier this week the M23 said it was ending its 19-month insurgency, hours after DR Congo government forces claimed military victory.
Reports say Sultani Makenga and about 1,700 fighters have been disarmed and are being held by the Ugandan military in Mgahinga, near the Congo border.
Earlier this week, Congolese officials said Col. Sultani Makenga had fled across the border to either Uganda or Rwanda.
Uganda has been hosting peace talks between the rebels and the DR Congo government. However, no peace accord has been signed.
Sultani Makenga is the subject of UN sanctions and it is unclear what Ugandan officials would do with him.
The M23 has wrought havoc across eastern DR Congo since it began its insurgency in April 2012.
Its fighters are mostly from the Tutsi ethnic group, a minority in eastern DR Congo but with ties to Rwanda’s leaders.
Their name refers to a 23 March 2009 peace deal which a former militia group – the CNDP – signed with the Congolese government. The rebels said the government had not lived up to its promises in the deal.
Analysts say the surrender of Sultani Makenga , if confirmed, will be a major success for the Congolese army which has been struggling to restore calm in eastern DR Congo for two decades.
Earlier this year the UN approved a new mission of 3,000 African soldiers with a mandate to fight the rebels.
They have the operational support of the existing UN Mission in DR Congo (Monusco) and have used helicopters to target the rebels, allowing the army to advance.
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