Government officials say at least 23 airports are closed, with landings and take-offs not permitted due to the lack of visibility.
Although common, the farmers' practice of burning areas is illegal in Bolivia.
However, the government has struggled to enforce the law, which was brought in to protect the environment.
The fires quickly spread due to dry conditions and high winds which carry smouldering embers through the air causing the subsequent blazes.
Speaking at a news conference on Thursday, Morales urged people not to burn fires indiscriminately.
"They say we are not equipped to fight the fires and it's true, we're not," he said.
"This isn't just the government's responsibility but every man and woman's.
"Those who burn off vegetation without thinking must first clear the area so that the fire doesn't jump across."
Buckets of water
The country's forest authority and land survey reported that up until Tuesday there were 25,000 heat sources from fires of various sizes, burning mostly in the east.
Fires have been detected in the departments of Cochabamba, Beni, Santa Cruz and Pando.
Television pictures showed fires burning across huge swathes of fields and residents attempting to tackle blazes with buckets of water and branches of brush.
Smoke from the fires has drifted as far as the highlands of La Paz.
Morales said he has instructed his cabinet to move forward on negotiations for the purchase of helicopters and on the managing of aid.
The president said he was also concerned about the affect that smoke was having on the environment.