KAMPALA, Dec 20 (Reuters) - Uganda's President Yoweri Museveni accused Lord's Resistance Army (LRA) rebel leader Joseph Kony on Thursday of not taking peace talks seriously, saying he had killed the top LRA deputy involved in the talks.

Museveni's comments followed numerous reports that Kony, whose 20-year rebellion killed tens of thousands of people and uprooted 2 million before a ceasefire last year, had shot dead his number two, Vincent Otti, accusing him of spying.

Otti -- who was seen as the brains behind the LRA, in contrast to the volatile Kony -- was a prime mover behind the rebels joining peace talks that began last year in South Sudan. Analysts worry his demise could set back the negotiations.

"Kony (is) not ready for peace," Museveni said in a communique published by his office. "He killed Otti. Who is he? Those that he is killing are Ugandans."

Deserters who fled LRA hideouts in northeastern Democratic Republic of Congo told of a rift between Otti and Kony culminating in the LRA leader ordering Otti's execution early in October. Many of Otti's supporters also fled in fear.

"The President said that although Otti had his own mistakes, he did a lot for the peace talks. ... He sadly noted that Kony could kill Otti while negotiations for peace were going on," the statement from Museveni's office said.

Aid agencies say Uganda's refugees have started to trickle closer to home as the north remains conflict-free after last August's truce. But many are wary of beginning their lives again, fearing that what was one of Africa's longest wars could reignite if talks fail. (Reporting by Tim Cocks; Editing by Daniel Wallis and Mary Gabriel)

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