One of the quakes, with a magnitude of 7.3, was felt as far away as Australia and sent small tsunamis into Japan's southeastern coast.
The first earthquake, with a magnitude of 7.6, struck at 4:43 a.m., about 135 kilometers, or 85 miles, from Manokwari, the main city in Papua Province. It struck at a depth of 35 kilometers, the U.S. Geological Survey said, and was followed by dozens of aftershocks.
At least four people died in Papua, and the airport runway near the epicenter was cracked, President Susilo Bambang Yudhoyono said.
Panicked residents in Manokwari fled their homes in the dark fearing a tsunami, said Hasim Rumatiga, a local health official. The Indonesian Meteorology and Seismology Agency issued a tsunami alert, but it was revoked within an hour after it was determined the epicenter of the main quake was on land.
A huge quake off the west coast of Indonesia in 2004 caused a tsunami in the Indian Ocean that killed about 230,000 people. Quakes centered onshore pose little tsunami threat to Indonesia, but those close to the coast can churn up large waves that sometimes reach the coastlines of other countries.
Power lines fell, cutting off electricity in and around Manokwari, and commercial flights to the area were canceled. The National Disaster Coordination Agency said 135 houses and buildings were badly damaged or collapsed.
"I've instructed emergency steps be taken to help our brothers and to restore power and other vital utilities," Yudhoyono said.
The Japanese Meteorological Agency said tsunamis from 10 centimeters, or four inches, to 40 centimeters high splashed ashore in towns along the coast. It also warned that bigger waves were possible.
Dave Jepsen, a seismologist at the government earthquake monitoring agency Geoscience Australia, said the quake was felt in the northern city of Darwin, 1,300 kilometers southwest of the quake. There was no damage, he said.
The relief agency World Vision Indonesia was flying in 2,000 emergency provision kits, including canned food, blankets and basic medical supplies, said a spokeswoman, Katarina Hardono.
Papua is the Indonesian portion of the island of New Guinea, about 3,000 kilometers east of the capital, Jakarta.
It is among the nation's least developed areas, and a low-level insurgency has simmered in the resource-rich region for years. It is off-limits to foreign reporters.
Indonesia straddles a chain of fault lines and volcanoes known as the Pacific Ring of Fire and is prone to seismic activity.