General Laurent Nkunda was a staunch ally of Rwanda
Security has been tightened at refugee camps in Rwanda after protests calling for rebel Laurent Nkunda's release.
Gen Nkunda, who claimed his fighters were protecting the Tutsi community in the Democratic Republic of Congo, was arrested by Rwanda last week.
A joint force of Rwandan police and soldiers put down the protests mainly by Congolese Tutsis, on Sunday - reportedly using live bullets.
Correspondents says demonstrations against the government are very rare.
A Tutsi like Rwanda's leaders, Gen Nkunda had guarded Rwanda's western flank against attacks from ethnic Hutu Interahamwe militias who fled there after the Rwandan genocide of 1994.
But in a change of policy, he was arrested after being invited by Rwanda to discuss a joint military force from both countries against Hutu forces.
DR Congo has allowed at least 6,000 Rwandan soldiers into its eastern region to help Congolese soldiers disarm the Hutu militia.
Rwanda, which hosts more than 50,000 Congolese refugees, has not yet said whether it will hand over its former ally to DR Congo, where he faces war crimes charges.
'Fighting for peace'
Thousands of Congolese refugees across Rwanda's two main camps - Kiziba in the south, and Gihembe in the north - took to the camps' street on Sunday in a co-ordinated protest.
They called the arrest of General Nkunda "illegal", and expressed their anger at the way he was reportedly trapped and arrested.
But a joint force of Rwanda police and army dispersed the protesters and many were injured in the skirmishes that followed.
"We could not go on with the demonstration as planned as the police and army stopped us," one man in Gihembe camp, which houses about 20,000 refugees, told the BBC.
"What we want is that Nkunda is released so that he goes back to DR Congo to continue fighting against the Interahamwe for he's our only hope for any return to DR Congo," he said.
"Nkunda was fighting for peace and we cannot understand why he was arrested."
In Kiziba camp, refugees claim that the army and police used live bullets and sticks to break up the demonstration.
One woman who was injured in the fracas said they were protesting peacefully when they were surrounded by police.
"They started beating us but we were not deterred by the beatings, for the anger we felt was more than the sticks' pain," she told the BBC's Great Lakes service.
"Shortly afterwards, they were joined by the army and started arresting young men among us. We tried to resist this and this is when they started shooting - that is how I got shot," she said.
The Rwandan authorities have not commented officially about the protests or commented on allegations that they were heavy handed in their attempt to quash them.
A refugee speaking to the BBC on Tuesday from Gihembe says the military have set up tents around the camp and intend to prevent further demonstrations.
Some 250,000 people have fled their homes in DR Congo's North Kivu province since August 2008, when Gen Nkunda began an offensive on the regional capital, Goma.
Human rights group have accused Gen Nkunda's rebel group - and also government forces - of numerous killings, rapes and torture.