The district will now enter a "recovery transition period" which will remain in force for 28 days.
Heavy rain caused flooding in the district on Monday and again on Wednesday after further downpours.
Waitaki Mayor Mel Tavendale agreed to lift the state of emergency just before midday on Thursday, a council update stated.
During the recovery period, "recovery managers" would have access to powers allowing them to close roads and public places, undertake works to stabilise land and properties, remove or secure dangerous structures and enter a property to rescue people or save lives.
Mrs Tavendale said: "The immediate emergency has passed, but for many people the impact of this event will continue for some time.
"Our focus now is on helping people recover, restoring services and supporting those whose homes, businesses and livelihoods have been affected."
The Emergency Operations Centre will remain active but its responsibilities will "increasingly" transition back to council's operational teams in the coming days.
