"Not all villagers in the dangerous radius are willing to evacuate. Until now there are still many people who remain in their houses," the disaster agency said, adding some were staying behind to protect gardens and livestock.
Spokesman for the BNPB Sutopo Purwo Nugroho said there was growing seismic activity around Mount Agung, indicated another eruption could occur soon.
The BNPB maintained a Level 4 alert on Tuesday, mandating no public activities within 10 kilometers of the peak.
Arie Ahsanurrohim, spokesman for Bali's largest airport, Ngurah Rai, announced early Tuesday morning flights would be grounded for another day over fears of volcanic ash.
All flights out of the airport are grounded until 7 a.m. local time Wednesday. More than 50,000 domestic and international passengers have already been stranded by the eruption.
The BNPB said there would be a re-evaluation of the decision to keep airports closed every six hours.
The main tourist centers are some distance from Mount Agung. Bali's artistic hub, the small town of Ubud, is about 50 kilometers (31 miles) southwest of the volcano, and Denpasar (where the airport is located) and the popular Kuta Beach are more than 63 kilometers (40 miles) away.
Tourists spoke to CNN of the travel chaos caused by the volcano, with some unable to leave Bali for three days.
Ash began spewing from Agung after it erupted three times on Saturday, beginning at around 5.30 p.m. local time. More eruptions followed on Sunday, with a "medium-pressure" event in the early evening.