"We have 45,300 people evacuating in several places as of Saturday morning," national disaster agency spokesman Sutopo Purwo Nugroho told AFP, adding that the number of displaced had almost doubled since Friday due to an influx of new data.
The shallow 6.5-magnitude quake earlier this week levelled hundreds of homes, mosques and businesses across Aceh province, one of the areas worst affected by the devastating 2004 tsunami.
Most of the displaced spent the night outdoors in tents near their ruined homes as hundreds refused to move into shelters fearing aftershocks, Nugroho added.
The army has established kitchens, shelters and a field hospital in the hard-hit town of Meureudu to help the region's overwhelmed health facilities.
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Indonesian President Joko Widodo visited Meureudu yesterday, pledging to rebuild the area's devastated communities as he called on Indonesians to pray for their countrymen.
The archipelago nation experiences frequent seismic and volcanic activity due to its position on the Pacific "Ring of Fire", where tectonic plates collide.
The province lies on the northern tip of Sumatra island, which is particularly prone to quakes.
In June a 6.5-magnitude quake struck off the west of Sumatra, damaging scores of buildings and injuring eight people.