The man, Constantin Tshidime Bulabula, will be brought before a military court in Kananga, Brig. Gen. Marcellin Assoumani Issa Kumba of the Congolese armed forces said.
Mr. Bulabula had been sought since he disappeared from his home in October.
The experts, Michael Sharp, 34, an American, and Zaida Catalán, 36, a Swede, were investigating crimes associated with a rebellion in central Kasai Province when they were abducted along with four Congolese colleagues in March 2017.
The bodies of Mr. Sharp and Ms. Catalán were found two weeks later, about 75 miles south of Kananga. The whereabouts of their colleagues are unknown.
Human rights groups have suspected the government may have played a role in the killings, and a United Nations inquiry in August could not rule out government involvement. Video footage of Congolese troops killing civilians in Kasai has led to at least seven arrests.
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The Congolese army has denied involvement in the experts’ killing. In April, the government released a video that it said documented the execution of the two experts. It identified the executioners as members of the Kamwina Nsapu militia.