The 7,000 ft-high volcano started erupting on Sunday morning, spewing ash and gases.
Officials from the Salvadoran environment ministry said there was a risk the volcano could erupt again, this time emitting a lava flow.
The last time the Chaparrastique spewed lava was in 1976. It also caused a strong tremor in the area in 2010.
During Sunday’s eruption a 5,000m-high ash cloud rose from the cone of the volcano. Since then, it has been emitting gases.
Volcanologist Francisco Barahona of the University of El Salvador said that a further increase in the emission of sulphur dioxide could be a sign that another eruption was approaching.
Another eruption “could trigger not ashes, but a lava flow”, Herman Rosa of the environment ministry said.
More than 2,000 people were evacuated after the first eruption on Sunday, but Civil Protection Director Jorge Melendez said almost half of them had decided to return to their homes against official advice.
Jorge Melendez said people had been “reluctant” to stay in the shelters provided, but he warned the authorities would use coercion in the case of an emergency.
Chaparrastique is one of more than 20 volcanoes in the small Central American nation.
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