The death could exacerbate a conflict that has already slashed the Andean nation's oil production and forced the government to relocate to a coastal city. More than 700 people have been arrested and more than 400 wounded, according to authorities, Presstv Reported.
The office of Ecuador's ombudsman, which monitors conflicts, said one protester was killed due to brain trauma on Wednesday. It added that it was investigating reports by indigenous group Conaie that other protesters also died during a police crackdown on Wednesday.
The government did not immediately respond to requests for comment.
The protests first erupted in the Andean nation of 17 million people a week ago when Moreno cut fuel subsidies as part of a package of measures in line with a $4.2 billion loan from the International Monetary Fund.
Conaie, which has mobilized several thousand members to Quito, blamed the "disproportionate and brutal repression" and said it was coordinating with other organizations to ensure there was no impunity.
Indigenous protesters, many of whom have walked from surrounding provinces to Quito, started to regroup near a park as police guarded government buildings early on Thursday.
However, there appeared to be fewer protesters than on Wednesday, when workers' unions and other social organizations joined the protest in a national strike that shuttered shops in Quito and other cities.
Graffiti criticizing Moreno and the IMF covered walls of buildings in Quito, as shopkeepers cleaned up streets littered with rocks and burned debris.
Moreno has refused to repeal the subsidy cut and said he would not step down.
Oil Minister Carlos Perez said the OPEC member nation had lost 520,000 barrels of production from the unrest, including 83,000 barrels from private companies for a total loss of $28 million, after protesters entered some fields.
Late on Wednesday, Interior Minister Maria Paula Romo apologized to the country after police fired tear gas near two universities and a cultural center in Quito where safe areas for protesters had been set up. She said police have faced extreme acts of vandalism from some demonstrators and thanked indigenous protesters for marching peacefully.
Moreno, 66, who succeeded leftist leader Rafael Correa in 2017, has relocated his government base to the coastal city of Guayaquil where there has been less trouble than in Quito.