The 68-year-old opponent and critic of longtime President Yoweri Museveni appeared in court in the capital Kampala on Friday looking frail and in a wheelchair.
He was briefly in hospital at the weekend and a government minister this week said his health condition was alarming.
His lawyers say he was "kidnapped" in Kenya's capital Nairobi with his aide Obed Lutale in November and returned to Uganda, where they were charged with offences including illegal weapons possession and treachery in a military court.
His wife said on February 12 that he had begun a hunger strike over his detention.
His lawyer said on Friday he had now ended it because his case had been transferred to a civilian court following a Supreme Court ruling on January 31 that trying civilians in military courts was unconstitutional.
The magistrates' court issued new charges, of treason and the concealment of treason - what it said were efforts to overthrow the government - but declined to allow Besigye to enter a plea because the offences can only be tried by a higher court.
He did not respond to the earlier charges as he viewed them as illegal.
His continued incarceration has elicited anger among Ugandans and sparked some protests.
The 56-member-state Commonwealth has called for his release.
Critics of Museveni, who took power in 1986, say Besigye's detention is the latest example of hardening authoritarianism ahead of an election next year in which the president is expected to stand again.
Officials deny accusations of human rights violations and say those detained are afforded due process through the courts.
Erias Lukwago, one of Besigye's lawyers, urged Chief Magistrate Esther Nyadoi on Friday to order prison authorities to take Besigye to a hospital for specialised medical care.
Nyadoi said her court did not have the authority to grant such a request.
