The money will go to the Manawatū Wanganui Regional Disaster Relief Fund Trust.
"I hope the Council contribution will encourage other local bodies and members of the community to make donations to the Trust too," Palmerston North Mayor, Grant Smith said.
The Trust was set up following the massive flood in the area in February 2004. The Trustees are made up of representatives from local authorities in the region. The Palmerston North City Council administers the Trust.
Palmerston North City Council staff are also on the ground helping with the recovery in Whanganui, including building and health inspectors, lifelines and relief emergency management officers.