“This year more than 4,000 soldiers and paramilitary officers will retire before December,” Conde said in a statement on national radio and television stations on Tuesday night.
Some aged police and customs officials also figure among those who will be retiring.
The retirement age in Guinea varies, but can go up to 65 for army generals.
Some of those who will be stepping down have been in the military since before independence from France in 1958, and are aged 70 or older.
They include soldiers who were discharged by former presidentLansana Conte (1984-2008) after a failed coup in 1985 and an army mutiny in 1996, and were later reintegrated by Sekouba Konate, who led a transition government from 2009 to 2010.
Guinea’s military has been a strong destabilising force since independence, with many leaders achieving power by coups until the nation’s first democratic elections in November 2010, won by Conde.
His first task has been to reform the defense sector, and an army which the International Institute of Strategic Studies estimated in 2010 has some 12,300 troops.
“This is not a witchhunt, but we need a change in mindset, which is difficult. All Guineans are set in ways which are not conducive to good governance,” said Conde.
He has raised the grade of the retiring officers to improve their retirement benefits, and said his government was carrying out a biometric census in government to do away with ghost employees and other irregularities.
Conde praised soldiers for “keeping calm and accepting sacrifices” since he took office.