Police said that during a targeted police operation in the Bugarama sector of Rusizi district to arrest the suspects "they turned violent, issued threats and attempted to flee".
Three other suspects were arrested, one of whom was wounded.
"Initial findings indicate that they were in a radicalisation campaign aimed at recruiting jihadists," the statement said.
"Radicalisation materials including audio CDs and text books were seized from the house."
Yesterday police said a "suspected terrorist" had been shot dead in Kigali during a three-hour shoot-out with officers.
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In January police shot dead a Muslim suspected of recruiting young people to join the Islamic State group in Syria when he reportedly tried to escape after being detained.
Police said at the time that "terrorist networks" were being set up in Rwanda and made a number of arrests.
Of those held, 23 are awaiting trial following a series of detention hearings, all of them held behind closed doors.
The country has never seen a jihadist attack but has been targeted in the past by grenade attacks, the latest in 2013. Those attacks were blamed by the authorities on rebels based in neighbouring Congo.