The development comes after the death or disappearance of some 30 people following deadly clashes between the Ugandan navy and Democratic Republic of Congo forces, which erupted on the lake late last week.
"Ninety-two Congolese fishermen have been arrested and are currently in prison in Uganda. 20 fishing boats and 25 engines have also been seized" by the Ugandan navy, the Congolese Fisheries and Livestock minister Paluku Kisaka said.
"In recent weeks, it had become a real business for the Ugandan navy. They systematically stop our comrades on the lake and make them pay large sums," said Jonas Kataliko, president of a local fishermen association.
"Those who resisted or refused to submit to the demands of the Ugandan military were thrown into prison across the border," he added.
Lake Edward, the smallest of the Great Lakes of eastern Africa, has seen a rise in tension between the two neighbours since the start of the year who disagree over the sharing of energy resources.
A Congolese delegation has been in the Ugandan capital of Kampala since Monday to negotiate an end to the tensions.
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