The eight men were arrested Tuesday during a police raid on the offices of the privately owned English-language Red Pepper and its local-language sister publications.
Yesterday the treason charge, which carries a possible seven-year jail term, was lodged against them.
The controversial article, published on Monday, said Museveni was plotting to overthrow his Rwandan counterpart Paul Kagame.
"The charges include treason, offensive communication and disturbing the peace of the president," Dickens Byamukama, one of the detained journalists' lawyers, told AFP. "All the staff denied the charges," he added.
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Among those being held is Red Pepper's CEO Richard Tusiime as well as chief editors and the financial director of the group.
Police spokesman Emilian Kayima confirmed the charges, without giving details; on Wednesday he had said the article was false and a threat to regional security.
Today, for the second day running, Pepper Publications tabloids were absent from newsstands.
Byamukama said the newspaper's offices had been sealed up and phones, laptops and other equipment confiscated.