Police managed to separate the two groups with what appeared to be tear gas.
Dadabai Osmanaliev, the head of Bishkek's Trauma and Orthopedics Center, told RFE/RL's Kyrgyz Service that four people were brought to his clinic, including three with pellet wounds.
Murat Sutalinov, the chairman of the National Security Service (SNB), later visited the scene of the clash. He denied opposition claims that the authorities may have provoked the incident.
"The clashes started and we had to interpose ourselves between them," he said. "We then proceeded to disperse the crowd. What else could we possibly do? They say this is a provocation on the part of the authorities. Who's making provocations? I wish they could go back to their home regions and demonstrate there. Bishkek has had enough of all this."
The incident broke out when several dozen people coming from Alatoo Square, where opposition demonstrators are picketing the presidential administration, proceeded toward a nearby square where some 500 government supporters were assembled.