Protests have continued in Bolivia's opposition-controlled eastern provinces despite Morales' 67 percent win in a nationwide recall vote earlier this month.
His proposals to redistribute farmland to the poor and overhaul the constitution have met with fierce resistance in these areas.
Energy Minister Carlos Villegas said on Thursday that Morales traveled to the Brazilian border town of Guajara Mirim after protesters occupied airports in the Bolivian cities of Riberalta and Guayaramerin, preventing the refueling of his helicopter.
Villegas was traveling with Morales in the region, where a new hydroelectric project is being studied.
"The best solution was to go by land to Guajara Mirim because there was an airport there that met all the security requirements with a paved runway and lighting," Villegas told local radio station Erbol.
Morales returned to the administrative capital
Villegas said the protesters had stoned the presidential helicopter earlier in the day, when Morales was miles away at the site of the potential hydroelectric plant.
Venezuelan President Hugo Chavez, a key Morales ally, and Argentine President Cristina Fernandez had to cancel a meeting with Morales in Bolivia's Tarija province in early August after dozens of protesters tried to storm the main airport there.
(Reporting by Carlos Quiroga; Writing by Hilary Burke, editing by Jackie Frank)