The raids come after the newspapers printed a leaked confidential memo by a senior general, David Sejusa Tinyefuza, alleging that President Yoweri Museveni was grooming his son Muhoozi Kainerugaba to succeed him and plotting to assassinate those opposed to the plan.
Several other generals -- among them police chief Kale Kayihura, chief of defence Aronda Nyakirima and Museveni's brother Salim Saleh -- condemned Tinyefuza's memo.
But Elly Tumwine, the most senior military figure in the country after Museveni himself, broke ranks by saying there should be no rush to condemn Tinyefuza and that he should be allowed to tell his side of the story. Tumwine was joined by Greg Mugisha-Muntu, another general and former army commander.
"This is a matter of national security concern," Okurut added.
The radio stations KFM and Dembe FM, both owned like the Monitor by the Nation Media Group and located in the same building, were also caught up in the raid.
"The police have refused to vacate our premises and to allow us to carry on with our work," the Red Pepper's chief executive officer Richard Tumusiime said in statement.
"This is a classic case of economic sabotage," he added, accusing the government of wanting to shut the paper for good.
Human Rights Watch said it was a "classic case of shooting the messenger".
"The authorities' heavy handed actions and shutting down of the newspapers and radio stations show blatant disregard for freedom of the press," HRW's Maria Burnett said.
The closure of the two papers means currently, the only major operating newspaper is the government owned New Vision.