Army spokesman Ronald Rvivanga told local media that two long-serving generals, Major General Aloys Muganga and Brigadier General Francis Mutiganda, had been sacked for "indiscipline."
"According to the law, this means that they have to hand over military equipment and leave the army without any benefits, because of what they did," he said, without elaborating.
Another 14 officers were also dismissed along with more than 200 others, the Rwanda Defense Force said in a statement.
On Tuesday, Kagame had announced a reshuffle in several top security posts, without giving any reasons for the move.
He said Juvenal Marizamunda had been appointed defense minister, replacing Albert Murasira who had served in the post since 2018.
The 58-year-old Marizamunda was previously the head of Rwanda's correctional services, and also a former deputy inspector general of police.
Kagame also appointed Mubarak Muganga as the new chief of defense staff, and Vincent Nyakarundi as army chief of staff, a statement from his office said.
Jean Bosco Ntibitura was named director general in charge of internal security in the National Intelligence and Security Services (NISS).
Other changes were also made to command roles in the Rwandan force which has been deployed in Mozambique since 2021 to counter a jihadist insurgency.
Of the sacked generals, Muganga had been appointed commander of mechanized forces in 2019, while Mutiganda had been in charge of external security at the NISS until October 2018 when he was called back to RDF headquarters in an unspecified role, local media reports said.
"He (Kagame) has also authorized the dismissal of 116 other ranks and approved the rescission 112 other ranks," the RDF statement said, adding that the moves were effective immediately.
Last week, the Democratic Republic of Congo's army accused the Rwandan military and the M23 rebel group of planning to attack the eastern DRC city of Goma.
The DRC has repeatedly accused neighboring Rwanda and its Tutsi-led government of backing the M23, a charge backed by several Western countries and independent U.N. experts, but one that Kigali denies.