More than 67,000 homes were desroyed or damaged in the worst-hit city of Palu, 1,500km northeast of the capital Jakarta, displacing 82,000 people.
Meanwhile a magnitude 7.3 quake has struck east of Papua New Guinea.
The U.S. agency has also deployed a team of disaster experts to coordinate humanitarian efforts, Nauert said, adding that the Department of Defense had also provided three C-130 transport planes that helped deliver up to 63 metric tons of disaster-relief supplies into the affected areas.
At least three people were killed as a shallow 6.0-magnitude quake struck off the coast of Indonesia's Java and Bali islands Thursday, a government official said.
A tsunami happened after the second quake hit the area in the afternoon of the same day.
" Almost 90,000 people were displaced by the quake, forcing them into evacuation centres across the rubble-strewn city".
The United States Geological Survey recorded the quake at magnitude 6.0.
Three people were crushed in their sleep when the natural disaster brought down buildings in the Sumenep district, in East Java.
Indonesia sits in the world's most tectonically active region, and its 260 million people are vulnerable to earthquakes, tsunamis and volcanic eruptions. "In other areas, the quake was felt to be moderate", reported Time.
The International Monetary Fund and the World Bank are holding annual meetings on Bali through Sunday. No tsunami alert was issued following the quake.
Indonesia suffered a powerful 7.5 magnitude natural disaster and tsunami last month on the island of Sulawesi killing more than 2000 people.
28 September on the Indonesian island of Sulawesi natural disaster of magnitude 7.5. Almost 2,000 people were killed in the disaster, as rescue workers had to dig through mud, rubble, and debris for dead bodies using their bare hands.
It struck the island of New Britain this morning, and the Pacific Tsunami Warning Centre said there is now a threat of a tsunami.
Agency spokesman Sutopo Purwo Nugroho said today prayers will be held, collectively, in Balaroa, Petobo and Jono Oge to "end the evacuation of bodies". "I immediately woke up and took my little kids out of the house", mother-of-two Ni Komang Sudiani said. "They asked to be relocated to another place and a house made for them".
After appealing for global assistance, Indonesia is now trying to limit foreign involvement in disaster relief.
'They say there is no need for aid in Indonesia.
The disaster agency, in a notice posted on Twitter, set the rules out for foreign non-governmental organizations (NGOs), saying they were not allowed to "go directly to the field" and could only work with "local partners".