A BBC reporter says two journalists were arrested and that others were beaten by officers using batons.
They had gathered to protest against the continued police occupation of the private Daily Monitor’s premises.
It and another paper were raided for publishing reports that the president was grooming his son to succeed him.
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This is a violation of media freedom and economic sabotage”
Geoffrey SsebaggalaProtester
They reported claims allegedly made by an army general that those opposed to President Yoweri Museveni’s son succeeding him risk being killed.
Mr Museveni, in power since 1986, is due to step down in 2016.
There has been long-standing speculation that his son, Muhoozi Kainerugaba, a brigadier in the army, is being groomed as his successor.
The government has denied having any such plans.
Evidence
The BBC’s Ignatius Bahizi, in Kampala, says Uganda’s Human Rights Network for Journalists had organised peaceful sit-down demonstrations outside the offices.
A crowd of about 100 journalists and activists had gathered outside the Daily Monitor on Tuesday morning, he says.
“This is a violation of media freedom and economic sabotage,” rights activist Geoffrey Ssebaggala shouted at police, AFP news agency reports.
Police chief Kale Kayihura told the BBC on Monday evening that the media houses – The Daily Monitor and Red Pepper – would remain closed until they co-operated with police.
The authorities want evidence of how the Daily Monitor got hold of the confidential letter, purportedly written by Gen David Sejusa, who is out of the country.
Daily Monitor managing director Alex Asiimwe told our reporter the paper would continue to refuse to reveal its sources.
Two radio stations, linked to the Daily Monitor, also remain off air.