Japan was first united around 300, but the first long lived political entity was the Fujiwara Era, from 645 to 1159.

This covered Honshu, with capitals at Nara and Nagaoka.

If you define civilization as anything above hunter-gatherer camps, then the Jomon period from 14,000 BC to 300 BCE is identified as the first period when pottery appeared. However these were probably predecessors of the Ainu rather than the modern Japanese. The sites so far identified have been primarily on the Tokyo Plain.