"We arrested 43 Rwandan suspects at the border with Tanzania on December 11. On further investigations two other suspects were arrested," police spokesman Emilian Kayima told AFP.
All have been charged "with carrying forged documents, false identities and the serious charge of terrorism as their intentions were pointing to that," he said without providing more details.
The suspects are being held at Nalufenya prison, east of the capital Kampala, often used to jail those accused of terrorism or involvement with rebel groups.
But Rwanda says they are members of the Rwanda National Congress, an opposition party in exile led by former allies of President Paul Kagame, that Kigali deems a terrorist organisation.
Neighbours Rwanda and Uganda have a fractious relationship, with their leaders competing for regional influence.
Rwanda has long blamed Uganda for harbouring dissidents.
Two days after the 45 arrests, Rwanda's foreign ministry in a letter pressured Uganda to charge the suspects.
The ministry accused Kampala of facilitating the recruitment of rebels and their travel to training camps, allegedly in eastern Democratic Republic of Congo.
Ugandan authorities say the loyalists were abducting and killing dissident Rwandan refugees, a claim backed by human rights groups but dismissed by Kigali.
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