Kampala, Uganda - Journalists at one of Uganda's leading independent newspapers were alarmed to find heavily armed police suddenly surrounding their building on May 20.

Brandishing Kalashnikovs, the police officers entered the premises, turned off two associated FM radio stations housed in the same compound, and ordered journalists away from their workstations. Staff at the Daily Monitor immediately posted pictures and commentary on Facebook and Twitter, where they learned a similar raid was also happening at the popular tabloid, the Red Pepper.

"I was shocked to see so many police at our premises. Like many colleagues, I thought they would soon leave," said Brenda Banura, a Daily Monitor reporter

Banura was mistaken, however. Nearly a week later, both newspapers remain closed and occupied by police, neither has been allowed to print, so both have been absent from newsstands across the country. The government-owned newspaper, the New Vision, has been the only English-language daily available to Ugandans during this period.

Police say they raided the newspapers to retrieve a letter and press releases written by a senior intelligence chief, General David Sejusa.

Police outside the Daily Monitor [Grace Natabaalo/Al Jazeera]

The classified letter, leaked to the Daily Monitor earlier this month, raised concerns about an alleged plot to assassinate senior government and military officials who are opposed Ugandan President Yoweri Museveni, who has been in power for 27 years, and his plans to hand over power to his son when he retires.

The Monitor originally published the claims of the assassination plot on May 7, and further infuriated the government by continuing to report on the controversy since.

Police say the leak of the letter was a crime, and so the media buildings are crime scenes. A magistrate's court issued the police with search warrants for both premises. Police also say the letter's intended recipients, two other senior security chiefs, did not receive copies, and so the letter must be retrieved.

General Sejusa, currently thought to be in London, issued press releases verifying the letter and denying knowledge of how it was leaked.

"The General's utterances had unfortunately stirred national anxiety, tended to generate public disaffection against some officers in the UPDF [Uganda People's Defence Forces], as well as the First Family," Minister of Information Karooro Okurut said in a statement. "This anxiety has the negative consequence of undermining national security."

Besides interrogating three journalists from the Daily Monitor, the police also secured a court order to compel them to reveal the source of the letter and information contained within it.

"We made it clear that that kind of cooperation will be hard to offer. It contradicts with our own laws in the Press and Journalist Act, which says you can withhold information if it is threatening the source," the Daily Monitor's Managing Editor Don Wanyama said.

The newspaper promptly appealed the court order, only to be surprised by the raid before the court could set the date for a hearing.

"We are horrified by this act, which is a gross disregard of Ugandan law and a violation of the Monitor's constitutional right," Daily Monitor's Managing Director Alex Asiimwe said in a statement immediately after the raid.

'Political shutdown'

Owners of Red Pepper have accused the government of a long-term plan to simply end reporting on topics of its choice.

This is a political shutdown. When you have a media siege going beyond five days it's aimed at achieving a political aim to make sure independent media do not speak out on issues that jeopardize political interests. Arinaitwe Rugyendo, an owner of Red Pepper newspaper

"This is a political shutdown. When you have a media siege going beyond five days it's aimed at achieving a political aim to make sure independent media do not speak out on issues that jeopardize political interests," one of the Red Pepper's owners, Arinaitwe Rugyendo, said.

The police defended its operation, and insisted its officers would not leave the premises until they found what they were looking for.

Hillary Onek, the minister for internal affairs, told parliament, "The interest of the police and other sister agencies is to get the letter published by the Daily Monitor, and given its security classification, investigate how the Daily Monitor got it, and possible violations of the law."

Until now the largest government crackdown on media by Museveni's government had been the closure of four radio stations in September 2009, in the wake of riots in the capital Kampala over a stand-off between the government and the kingdom of Uganda's largest ethnic group, the Baganda.

In October 2002, police conducted a similar raid on the Monitor and shut it for nearly a week, following publication of a story that claimed an army helicopter had crashed while fighting the rebel Lord's Resistance Army.

President Museveni, who late last year threatened to close media establishments for "writing lies", has not publicly commented on the latest closures. While Ugandan journalists are no strangers to harassment by state officials, many found the government action drastic and defenceless, and took to Twitter to condemn it.

On Twitter, using the hashtags #Monitorsiege, #RedPepperSiege, and #MediaSiege amongst others, Ugandans asked why the government was going for the messenger instead of dealing with the author of the letter and the issues he raised.

@pmagelah tweeted, "Please [Uganda Police] stop being cowards go for Gen Sejusa the author of letters & not the messenger daily monitor." @btabaire wrote, "Museveni displays arrogance of power and regime decadence in raid on media ... 27 years in power does that."

The Uganda police simply tweeted it would continue its operation until the letter is found.

But there has been no let up in criticism of the police action. Human Rights Watch's Maria Burnett said the Uganda government was using abusive tactics to scare journalists away from politically sensitive stories.

"This Daily Monitor raid is a classic case of shooting the messenger," Burnett said. "The authorities' heavy-handed actions and shutting down of the newspapers and radio stations show blatant disregard for freedom of the press."

Sarah Jackson, Amnesty International's deputy Africa director, echoed the sentiment.

"The police must immediately withdraw from the offices of all media outlets targeted in this disturbing crackdown, and allow them to go about their journalistic work," said Jackson.

The 2013 press freedom ranking by Reporters Without Borders put Uganda in 104th position out of 179 countries.