BNPB's official death toll from Sunday's quake stood at 131 on Wednesday, although some Indonesian officials put the number at 347.
Officials said the epicenter of the aftershock was on land and so there was no risk of a tsunami.
The Indonesian island of Lombok has been hit by a strong tremor, as the search continues for victims of Sunday's quake.
A magnitude 6.2 aftershock rocked Indonesia's Lombok on Thursday, sparking fresh panic on the tropical tourist island after a series of tremors that have killed more than 150 people in the past two weeks.
Lombok experienced another natural disaster on Thursday, an aftershock of magnitude 5.9.
The 5.9-magnitude quake struck at a shallow depth in the northwest of the island, the US Geological Survey said.
TRT World spoke to Jack Hewson who is following the updates from capital, Jakarta.
In northern Lombok, some people leaped from their vehicles on a traffic-jammed road while an elderly woman standing in the back of a pickup truck wailed "God is Great".
Twenty-four people were injured by falling debris in the tremor, Nugroho said.
It was the strongest of some 355 aftershocks that have rattled the island since Sunday, national disaster agency spokesman Sutopo Purwo Nugroho said.
Nyoman Sidekarya, chief of the provincial search and rescue agency that covers the Indonesian island of Lombok, tells The Associated Press that the death toll from the quake that hit the island on Sunday is now 227.
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Indonesia's top security minister says the death toll from the quake on Sunday has risen to 319, according to The Associated Press.
Sunday's quake came only days after a slightly smaller one, which killed at least 16 people.
A strong aftershock has shaken the Indonesian island of Lombok, causing the collapse of several buildings.
"When the quake happened, I took my kid and ran", she said.
Sumiati, 27, was giving birth as the quake hit, and had to flee with her one day old baby to an evacuation spot.
Evacuees at a shelter in northern Lombok's Tanjung district ran onto the road crying and screaming, witnesses said.
The death toll following the natural disaster on the Indonesian holiday island of Lombok on Sunday is now at 227, according to the chief of the provincial search and rescue agency.
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