The move also comes two days after the motorcade of right-wing President Daniel Noboa was pelted with stones by a group of about 500 people protesting rising fuel prices.
"Military personnel, air and ground resources have begun a large deployment toward the city of Quito" in order to "safeguard security" there, army officials wrote in a WhatsApp group with journalists.
The country's largest organization of Indigenous peoples, called Conaie, have blocked roads -- including in the capital's Pichincha province -- since September 22.
One protester has died, around 160 injuries have been reported, and more than 110 people have been detained, human rights groups and officials said.
Past Conaie-led protests have led to violence in the capital, causing the overthrow of three presidents.
Conaie's leader Marlon Vargas said recently that if necessary, his supporters would "take over" Quito.
Noboa clapped back, saying "no one can come and forcibly take over the capital."
Noboa emerged unscathed from the motorcade incident, which his defense minister described as an "assassination attempt."
One official said Noboa's car bore bullet marks.
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