Some 3,650 schools -- about 15 percent of the national total -- have been closed until Friday, minister Edgar Pary told reporters.
The Santa Cruz region, Bolivia's economic engine and most populous region, has been most affected.
It is a common practice to set fires to free up forest land for farming.
According to the environment ministry, some two million hectares (4.9 million acres) of forest and grassland have been burned this year.
The skies over the capital La Paz and the second city of El Alto, which hosts the international airport, were blackened by smoke Wednesday.
Health Minister Maria Rene Castro said health warnings have been issued, including a recommendation for people to wear face masks, reduce physical activity, and for the elderly, children and pregnant women to stay indoors.
The work of firefighters has been made more difficult by a shortage of water in Bolivia in the midst of drought.
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