The opposition legislator and 11 others were freed on a 'non-cash' bail on Monday.
The court did not approve the bail application of more than 10 other suspects charged alongside the MP.
Kyagulanyi, who is better known by his stage name, Bobi Wine, has been charged with treason.
They were arraigned over their alleged role in the pelting with stones of the President Yoweri Museveni's convoy after a local election rally.
Military prosecutors on Friday dropped weapons possession charges against Kyagulanyi.
A civilian magistrate ordered Kyagulanyi remanded in custody until August 30 and granted him access to private doctors citing the "health of the accused", according to footage broadcast on state channel UBC.
Kyagulanyi had been arrested since his arrest on August 14.
|Protesters have been demonstrating against the arrest and detention of Bobi Wine [Reuters]|
The popular musician has emerged as an influential critic of Museveni after winning a seat in parliament last year.
The 36-year-old opposition legislator has used his music to address the country's political and social issues.
In recent days, Uganda's government has faced pressure to free Kyagulanyi, with dozens of musicians around the world speaking out against his alleged beating in detention.
Security forces in recent days have violently put down street protests by Ugandans demanding his release.