In a televised address last Thursday after the congressional vote, Morales said: "If we politicians can't agree, it is better for the people to decide the country's destiny."
The decision comes a week after voters in the country's richest region, Santa Cruz, voted for autonomy from Morales' leftist government in a referendum.
Morales, who has condemned autonomy votes as divisive and illegal, asked for all of Bolivia's nine regional governors to meet him to avoid further division.
However, those of the eastern lowland regions of Tarija, Beni and Pando, which also plan autonomy referendums before the end of June, said they would not meet Morales until after their votes have gone ahead.
|"Autonomy must be for all Bolivians, with social justice, not autonomy just for groups"|
Evo Morales, Bolivia's President
The referendums pit the wealthier eastern part of the country against the western highlands, where Morales, Bolivia's first indigenous president, has his support base.
Speaking in Santa Cruz, Morales said: "This Bolivian family cannot be divided. Autonomy must be for all Bolivians, with social justice, not autonomy just for groups."
The terms of Morales and Alvaro Garcia Linera, the vice-president, formally end in January 2011 but could be cut short if more than 53.74 per cent of voters reject them.
The vote on Morales's rule is meant to show who has the support of the people.
The opposition, however, is banking on winning the vote of confidence, riding on a tide of support shown in the Santa Cruz referendum, where 85 per cent of voters backed more autonomy from La Paz, Bolivia's seat of governance.
The autonomy referendums are widely seen as a rejection of Morales' policies, particularly his goal of redistributing lands to Bolivia's poor, indigenous majority.
His pro-indigenous policies worry the wealthy eastern provinces, where some large landowners see him as a threat to booming agriculture.
The referendum votes would in theory give conservative-leaning regions more control over natural resources and the tax and justice systems.