The arrest of opposition leader Kizza Besigye has sparked running battles between his supporters and Ugandan police firing tear gas and bullets.
Dr Besigye was arrested three weeks after returning from a four-year exile.
He has been charged with treason, as well as the alleged rape of a woman in 1997. Mr Besigye denies alleged links to two rebel groups.
Dr Besigye is seen as the strongest challenger to President Yoweri Museveni in elections due next March.
He was arrested after addressing a rally just outside the capital, Kampala before being escorted to a police station in the centre of the city.
Several cars and shops were set on fire as disturbances spread out from the city centre.
Suleiman Kiggundu, chairman of the Forum for Democratic Change (FDC), which is sponsoring Dr Besigye in the election, condemned the arrest.
"This is a barbaric act that we are witnessing. This is a savage act," he told the AFP news agency.
"We are not going to take this taking lying down. We are also going to use all means, political, legal and any other," he said. "We are going organise people to demonstrate against this."
Some opposition figures see the charges as an attempt to stop Dr Besigye from contesting next year's poll.
Once Mr Museveni's doctor, Dr Besigye ran against the president in 2001 before fleeing, saying his life was in danger.
On his return to Uganda last month, Mr Besigye told reporters that the time was right to return and take on what he termed "the dictatorship".
The government has often linked Dr Besigye's name to the People's Redemption Army, a rebel group allegedly based in the lawless eastern Democratic Republic of Congo.
Dr Besigye has denied any link with the group, but in past interviews has threatened to go to the bush to overthrow the government.
Police chief Major General Kale Kayihura on Monday also accused Dr Besigye of links to the brutal Lord's Resistance Army which operates in northern Uganda.
Besigye (in blue cap) used to be Yoweri Museveni's doctor
"His public statements, justifying violence and refusing to renounce armed rebellion, confirmed the suspicion he was actively involved in acts of war against Uganda," he said.
If found guilty, he could face the death penalty.
Shortly before Dr Besigye's return, Mr Museveni wrote to his cabinet colleagues, saying Dr Besigye could face criminal charges.
In the letter, leaked by cabinet minister Moses Ali, the president says he is not opposed to Dr Besigye returning to Uganda.
But it continues: "However, I am reliably informed that he may have long-standing criminal charges that would be brought against him. The cabinet needs to be aware of that."