The Mali president and prime minister were banished by police officers who led the coup last year and became vice presidents of the caretaker government.
Colonel Assimi Goita states that President Bah Ndaw and Prime Minister Moctar Diouf have failed their mission and are trying to thwart the transition of the country.
They were arrested hours after a government remodeling that was replaced by two senior army officers.
Colonel Goita says the elections will continue as planned next year.
But he ignored the plea for the unconditional release of presidents and prime ministers from the United Nations leaders, the African Union, the Economic Community of West African States (Ekowasu), the EU and the United States.
The two have been detained in a military camp outside the capital, Bamako, since they were arrested on Monday night.
What caused the crisis?
Beverly Ochieng, BBC Monitoring
Colonel Goita said he had not been consulted on the cabinet reshuffle and said he was supposed to be the Vice President.
After last year’s coup, military junta leaders sought to lead a caretaker government overseeing the transition to civilian rule for 18 months.
However, Ecowas, the regional organization that brokered the transition agreement, claimed private leaders.
Still, Colonel Goita remains a true power broker in the apparently volatile West African nation.
The dismissal of Ibrahim Bubaka Keita as president last year was generally celebrated.
It was followed by weeks of anti-government protests over heightened anxiety, allegations of corruption, and economic decline.
However, tensions are rising due to the slow pace of change over the last nine months.
A major union strike is in its second week and could cripple the economy.
In the face of these issues and the threat of new protests, the caretaker government has agreed to appoint a new, broader cabinet.
Colonel Goita wasn’t the only one upset by the remodeling. The opposition group M5RFP behind last year’s protests was also furious at the unrewarded ministerial status.
What will happen next?
In the capital Bamako, a delegation from Ekowasu is expected.
Last year, it threatened sanctions unless a civilian caretaker government took over from the military.
Now that Colonel Goita has responsibly abandoned the agreement, it is not clear what the consequences will be.
He asks people to start their business as usual and promises that the military will commit to a tentative arrangement.
Also, it is not yet clear what the M5 RFP will do with this move. Due to growing dissatisfaction, he was threatened to return to the street in early June.
The group was critical of the prime minister.
Why is Mali so unstable?
Reforms are difficult to implement quickly, vast landlocked countries are poor, and most are undeveloped.
A pre-2012 coup led to extremist Islamists taking advantage of the turmoil and occupying the northern part of the country.
French troops helped regain territory, but attacks continue as rebels take advantage of the region’s persistent political unrest.
All this undermined public confidence in the ability of military leaders to confront the Muslim rebellion that spilled into neighboring Burkina Faso and Niger.