They mostly stay in school gymnasiums and other public facilities while 3,460 prefabricated houses are being erected to accommodate them, a spokesman for the Niigata prefectural office said.
"It will be quite tough for them to live in gymnasiums in the winter as snow could pile as high as three meters (10 feet)," Atsushi Moriyama said.
The official said 767 people were living in tents or vehicles since they refused to shelter in buildings after losing their houses. "We have been advising them to come out and stretch to relieve themselves of stress. I also encourage them to join others in public facilities," the spokesman said
A total of 40 people died in the October 23 quake, which registered 6.8 on the Richter scale, and in numerous aftershocks in the rice-growing region some 200 kilometers (125 miles) north of Tokyo.
Some died from thrombosis in the lungs and other ailments developed by squeezing themselves into compact spaces such as cars for a long time.
Police say 3,180 people were injured in the deadliest earthquake to hit Japan since 1995, when 6,433 people were killed in the western city of Kobe.
A memorial service was held on Tuesday in Ojiya where 12 people died of quake-related causes.
A mild tremor, registering 3.6 on the Richter scale, rocked the region at around 2:00 pm (0500 GMT) on Tuesday, the Meteorological Agency said, bringing the total of aftershocks in Niigata to 801.
"The possibility of an aftershock of the magnitude-5 class occuring will be extremely low by mid-December. But an earthquake of the magnitude-4 class may possibly occur," said an official at the agency's seismic division.