The council of ministers also discussed the possible mobilization of reservists, they said late on Wednesday.
Following the decision, taken by junta leader Assimi Goita, to cancel the festivities, the anniversary will be "celebrated in sobriety and in the spirit of national revival," the council said in a statement.
Goita ordered the government to allocate the funds planned for the festivities to help the victims of a series of recent attacks and their families, it said.
Mali, which was in 2012 plunged into turmoil by independence and Salafist insurrections in the north, has this week seen a resumption of hostilities by predominantly Tuareg armed separatist groups.
On Tuesday, they launched an offensive against army positions in the garrison town of Bourem, which the army said it had repelled.
The two sides provided contradictory reports of events, but both reported dozens of deaths.
The renewed military activity by the Tuareg separatists has coincided with a succession of attacks attributed mainly to the Al-Qaeda-linked jihadist alliance Support Group for Islam and Muslims, GSIM.
It also coincides with the ongoing withdrawal of the United Nations stabilization mission MINUSMA, which is being pushed out by the junta after 10 years of deployment.
Several recent attacks claimed by GSIM have killed a number of soldiers, including in the town of Bamba on Sept. 7 and the city of Gao on Sept. 8.
An attack on a passenger boat on the Niger River, blamed on jihadists, left dozens of civilians dead last week.
Goita expressed his "deep distress" at the losses caused by "the savage and barbaric attack against the boat (and) the assaults on the camps in the towns of Bamba, Gao and Bourem," the council of ministers said.
It was his first public remarks on the boat attack.
Mali, a former French colony, became an independent republic on Sept. 22, 1960.