Zaw Min Tun, a junta spokesperson, said in a statement on Thursday that the Myanmar leader was kept in solitary confinement in accordance with criminal laws.
Ms Suu Kyi was arrested on 1 February last year after the military toppled her elected administration and took control of Myanmar.
The leader was put under house arrest in the capital but was later moved to another location in the capital, thought to be a military base.
The Nobel Peace Prize laureate was arrested on multiple charges and is facing at least 11 corruption counts at a special court in Nay Pyi Taw.
She could face up to 15 years in prison.
On Wednesday, legal officials said her cases would be heard at a new facility constructed in the prison compound.
Ms Suu Kyi has already been ordered to 11 years in prison over charges of illegally importing and possessing walkie-talkies and violating Covid safety protocols.
She has also been charged with election fraud and violating the Officials Secrets Act.
The move by the Myanmar government triggered backlash from human rights organisations and activists who slammed the decision.
Amnesty International called the move “deeply concerning”.
“The Myanmar military’s order to transfer Aung San Suu Kyi from house arrest to prison is deeply concerning. Prisons in Myanmar are notoriously inadequate when it comes to respecting basic human rights. Prisoners are subjected to inhumane conditions and deprived of dignity,” said Amnesty.
The junta spokesperson claimed in the statement that the prison was in “good condition”.
The 77-year-old has already spent about 15 years in detention under the previous military administration’s rule.
Her supporters have called the charges against her as politically motivated and an attempt to keep her away from returning to the political sphere.