This was creating "slow but persistent showers" in the area, he said.
There was a risk of thunderstorms possibly setting in later but the weather would clear up tomorrow, he said.
The Whakatāne District Council posted on their Facebook page that they had received reports of surface flooding in some parts across the region.
The New Zealand Transport Agency was reporting that State Highway 2 near Waiotahi was under stop and go traffic management due to a slip between Ohiwa Beach Rd and Pohutukawa Dr.
Fire and Emergency NZ received two weather-related callouts this morning.
The first was in Matatā about 7.40am where crews were called to flooding at a Pakeha Rd property as a result of the rain, a Fire and Emergency NZ spokesman said.
While the second was reports of flooding in a building on Ohiwa Beach Rd in Waiotahi about 10.18am, he said.
Both were quickly resolved.
The MetService weather forecast for Whakatāne showed the rain should clear this afternoon with a high of 24C expected.
Tomorrow was looking fine all day with a high of 26C.