Niger's Defence Ministry said that 72 mutineers had escaped and 217 were arrested in the taking of the garrison in Ngourti, 1,600 kilometres (1,000 miles) east of the capital, Niamey.
Two government soldiers were reported killed and two injured in the assault.
''The military mission has been able to achieve the restoration of order and discipline in all the barracks," the ministry said in a statement read on television.
Capital threatened
It also announced an investigation into the mutiny, during which troops from three south-eastern garrisons took several hostages.
Government troops were sent to the Diffa region and last Saturday recaptured the army barracks in Diffa town.
On Monday, the mutiny spread to soldiers based in Niamey, but this was quickly put down.
Rebels from Diffa fled to the garrison at Nguigmi, but that was retaken by government troops on Tuesday.
Several army officers who had been taken hostage were released.
Some of the rebels were thought to have fled to northern Nigeria, where local people speak the same Hausa language and have close trading relations.
'Grave act'
Police in the northern Nigeria state of Yobe were on high alert to prevent the rebels entering.
The authorities there approved funds for special police squads to patrol the frontier.
Earlier in the week, Niger had asked the Nigerian authorities to send back any mutinous soldiers.
Niger's President, Mamadou Tandja, said "exemplary action" would be taken against all those found responsible for Monday's uprising in Niamey.
He called the uprising an "extremely grave act" which could have pushed the country to the brink of civil war and said it undermined Niger's credibility at home and abroad.
There have been several army mutinies over living conditions. Soldiers are paid about $35 (£23) a month.
The army has also staged several coups but not since Mr Tandja was elected in 1999.