Tap water to some Castlecliff homes should now be running clear as contractors work to fix the city's water supply.

Whanganui's water has been running discoloured since Wednesday afternoon after dirty water entered the reticulation system following emergency repairs.

Castlecliff appears to have been affected first with the problem spreading across the city.

"We have been advised by contractor, Veolia, that the supply from Longbeach Dr to Manuka Street within the Castlecliff area is now clear and we are moving to other areas such as Springvale and Otamatea," Whanganui District Council said in the written statement on Thursday afternoon.

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"We are hoping to have most areas completed within a couple of hours."

The council says the water was safe and is still being chlorinated.

"Veolia contractors are working on flushing the mains in the affected area and will continue until the system is clean.

"After investigation it appears this has come from an emergency repair completed early yesterday morning.

"Unfortunately dirty water has entered into the reservoir and then gone out into the reticulation affecting Castlecliff."

After earlier on Thursday advising residents did not need to run, people are now advised to run cold taps for 10 minutes to flush out any discoloured water.

If it is not clear after 10 minutes people should call Council Infrastructure on 06 349 0001.