State Highway 90 between Tapanui and Waikoikoi in Otago has reopened after being closed by flooding on Sunday.

Waka Kotahi / New Zealand Transport Agency said the road reopened shortly after 11am on Monday.

But the agency warned road users needed to be cautious while driving in the region with heavy rain still falling.

An orange heavy rain warning was in place for the headwaters of Otago's lakes and rivers, and an orange strong wind warning was in place for the Canterbury high country.

Snowfall warnings are also in place for the Milford Road on State Highway 94, the Crown Range Road, Lewis Pass and Arthur's Pass.