Speaking during a national address on Saturday, Museveni questioned why Besigye had not allowed the criminal proceedings against him to progress, arguing that a trial would provide him with an opportunity to challenge the government's case.
"Besigye has created drama in courts of law. Why should the legal system for so long allow an accused person to just refuse to be tried? Is that a good system?" Museveni asked.
The President further argued that if Besigye believed the charges against him were politically motivated, the courtroom was the appropriate place to prove his innocence.
"Why would this great democrat and human rights fighter, Dr Kizza Besigye, spend so many calories on refusing to go to trial where he would have the opportunity to prove his innocence and expose the undemocratic behaviour of Museveni and his family?" he said.
Museveni also claimed that it was "almost two years" since Besigye's arrest and alleged that the opposition leader had spent that period refusing to face trial and misusing the legal process.
However, Besigye's case has undergone several significant legal turns since his arrest.
Besigye and his aide, Obeid Lutale, were arrested in Nairobi in November 2024 and initially charged before the General Court Martial with treason and misprision of treason.
The proceedings before the military court were later overtaken by a landmark ruling of the Supreme Court of Uganda, which declared that civilians cannot be tried by military courts. The judgment forced the state to discontinue the court martial proceedings against Besigye and file fresh charges before the civilian courts.
The case was further delayed earlier this year when Besigye embarked on a hunger strike to protest his continued detention beyond the constitutional limits. His deteriorating health prompted urgent court proceedings and renewed public debate over his prolonged incarceration before trial.
Since the transfer of the case to the civilian justice system, disagreements over legal representation have emerged as another major point of contention.
When Besigye appeared before court on Wednesday, he maintained that he wanted former Kenyan Justice Minister Martha Karua to lead his defence team, working alongside Kampala Lord Mayor Erias Lukwago.
Karua, however, was deported to Kenya by Ugandan authorities and declared persona non grata despite publicly stating she had travelled to Uganda to represent Besigye in court.
Lukwago, meanwhile, was arrested and remains in custody on allegations of misprision, leaving Besigye without the two lawyers he had identified to lead his defence.
Addressing court on Wednesday, Besigye said he had instructed the remaining members of his legal team to withdraw from representing him because he did not want them to face arrest over their involvement in his case.
He has also made it clear that he does not intend to appoint a new lead lawyer in place of Karua and Lukwago, setting up yet another legal impasse as the state seeks to proceed with the civilian trial.