Flooding from heavy rain is affecting state highways in Otago and Southland, with one highway completely closed and others partially blocked.

NZ Transport Agency Waka Kotahi (NZTA) said State Highway 90 between Tapanui and Waikoikoi was closed due to flooding.

Both southbound and northbound traffic has been impacted, with motorists advised to allow extra time for travel.

A detour has been put in place with southbound traffic advised to turn right onto Station Road, then on to Seddon Hill Road before turning left onto Koi Road and returning to SH90.

NZTA said the reverse applied for northbound traffic.

MetService has issued an orange heavy rain watch for the headwaters of the Otago lakes and rivers from noon tomorrow.

Flooding from heavy rain is affecting state highways in Otago and Southland. Photo / NZTA

A heavy rain watch is also in place for the headwaters of the Canterbury lakes and rivers from 3pm tomorrow.

NZTA said other highways in the region may be down to one lane or partially blocked.

It said people should take note of signage and take care where there is water on the roads.

On wet, slippery roads, motorists are advised to reduce speeds, increase following distances, watch their visibility and brake carefully.