Civil defence director Jorge Melendez said a yellow alert had been issued and investigators had been sent to the area to look for signs of fresh lava, but that none has been detected so far.
"We have implemented emergency measures to evacuate villages located within 3 km (1.8 miles) of the volcano," He said.
Shelters have been set up for the evacuees, but Mr Melendez said some inhabitants had been reluctant to leave their homes. "One has to leave for one's own safety," he said.
Assistant health minister Eduardo Espinoza said two people had been treated at hospitals for respiratory problems apparently linked to the eruption yesterday, "but we do not have any serious cases to report".
He said: "We are providing assistance to people evacuating, and we are asking them to protect themselves against the gases, which can affect the respiratory tract."
He also urged people living near the volcano to avoid drinking from local water sources.
The 7,025ft volcano is located about 90 miles east of San Salvador, the capital. Its last significant eruption was in 1976.
San Miguel is one of the country's largest cities and is located 30 miles from the volcano.
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