President Museveni has promised to withdraw the army from the water bodies and hand over the administration of fishing communities to the "elders".
Mr Museveni, who was on Tuesday campaigning for Ms Janet Adongo at Amatiburu Primary School in Kangai Subcounty, Dokolo, in the district woman MP by-eleciton, promised to take decisive actions against soldiers implicated in extortion of locals.
"In the month of May, I want you the people who are near the lakes to guide me, to get the elders of this area; they should be the ones to tell us who is spoiling the lakes so that the army can go away and the people themselves look after the lakes," Museveni said.
"The minister for Northern Uganda can coordinate them; the ones from this side, Nakasongola side and Busoga side, we shall have a conference and then we can remove the soldiers from the lakes," he added.
The Fisheries Protection Unit (FPU) was formed by President Museveni in January 2017 to mitigate and end illegal fishing practices on Ugandan water bodies.
While its operations has largely helped to restore the hugely depleted fish stock, especially the Nile Perch and tilapia in the country's water bodies, FPU's operations have always come under intense scrutiny over allegations of human rights violations, among others.
The President on Tuesday called upon citizens to report soldiers who are extorting money from fishermen so that they are disciplined.
"If you have evidence about soldiers who are extorting money, bring the evidence and we arrest them. We don't have to wait until the handover. People need to be assisted to do proper fishing," President Museveni saod.
"And the ones who are saying that I should just take away the soldiers, I'm a bit suspicious of you because why don't you want a proper handover? You have admitted that there was immature fishing because of the problems which you had.
"That's why I was forced to bring in soldiers. I am the one who has proposed here that if the elders can come and take charge,
"I can pull away the soldiers and then hand over the lakes to the elders but for you're saying you just go, don't handover. No, that's not how things are done. I'm a bit suspicious of you. Maybe you are the one eating young fish and they want me to take away the soldiers so that they finish the fish before the elders come in. This is very dangerous for your country," Museveni noted.
The issue of alleged extortion by the army on the fishing communities had earlier been raised by Hon. Felix Okot Ogong, the Member of Parliament for Dokolo South, as one of the many challenges that needed urgent intervention because it was greatly affecting the support of the NRM party.
"Your Excellency, our people in the fishing communities are requesting you to remove the military from the waters so that the local people can take charge themselves. These soldiers are extorting money from the fishermen," Hon. Ogong said.
President Museveni told the locals that he was forced to bring in the army to save the fishing industry which was on the verge of collapsing as fishermen had resorted to fishing immature fish. He further reported that despite a few mistakes by the army, the fishing industry is coming up again.
"But you have allowed the lake to be invaded by even foreigners, I hear; people who come from other parts of the world and eat the young fish. If the Banyankore were eating the calves, there would be no cows, all the cows would be finished," the President noted, adding that, when the fishing industry was doing well, Uganda had 22 factories for fish processing and earned almost $200 million from fish.
"Now by the time I brought in the soldiers, all factories had closed except eight (8). And now when these people- the soldiers came in, even though they're making mistakes, the fish had come back somehow. Now 12 factories are working instead of eight.
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When you see me building schools and roads, I'm using money from fishing and other sources of wealth. So, when you say it doesn't matter, let the factories close because we have eaten young fish, then you are an enemy of Uganda, you're not a friend. I don't want leadership of lies and darkness, finding people in mistake and encouraging them, the country collapses," Gen Museveni reiterated.
He further assured the fishing communities that after meeting with the elders, they will be guided on how to protect the lakes and the fishing business.
"The elders fortunately are still there, we shall organise, hand over to them and chase away all the others because I don't think people should come from neighbouring countries and go to the lake. Why don't the nearby people be assisted to do proper fishing? If that one is done, then I will be very comfortable," Museveni said.
