The marchers were headed from the north of the city to its historic center, where a large number of security forces have deployed following violent clashes on Tuesday.
Demonstrators were trying to reach the San Domingo central square, just a few blocks from the government headquarters being protected by security forces, said Apawki Castro, a spokesman for the indigenous umbrella group CONAIE.
The government, which declared a state of emergency last week, announced earlier Wednesday it would not allow the protest to pass through the city center.
Moreno scrapped fuel subsidies as part of an agreement with the International Monetary Fund to obtain loans despite Ecuador's high public debt.
The subsidies were costing the government $1.3 billion a year.
The IMF agreement, signed in March, allowed Ecuador to borrow $4.2 billion.