Roads were closed in the worst-affected areas.
Council spokesman Alan Beuzenberg driving quickly through flooded areas could push water on to properties and put houses at risk.
Banks Peninsula was worst-hit, with the tourist town of Akaroa receiving a massive 185mm of rain in the last 24 hours, resulting in number of slips and trees coming down on to roads.
Canterbury St in Lyttelton has been sand-bagged and there are a number of slips on the road between Lyttelton and Governors Bay.
The eastern suburbs around the lower reaches of the Avon and Heathcote rivers and areas around the Lower Styx River burst their banks in parts and caused flooding.
Dudley Creek and St Albans Creek also overflowed and contractors were sand-bagging to protect some buildings.
MetService spokesman Dan Corbett said a rain warning will remain in place for much of Canterbury and Otago until tomorrow.
He described the weather front as "sitting and spinning like a car stuck in the mud" and but should ease later today.
The respite will be brief, however, with a second front arriving in Canterbury from the Gisborne area mid to late tomorrow for another burst before easing.
Across the north and west of the North Island, there are likely to be showers over the next several days, some of which may be heavy.
While the weather is set to improve later in week, it will only be in time for another large Tasman Sea low to take aim for New Zealand, bringing more flooding and slip risks, says forecaster WeatherWatch.co.nz.
Heavy rain has been a constant threat since mid-July, but head weather analyst Philip Duncan said the incoming low for this Sunday and Monday may be the last of the big lows of the winter.
Models show more spring-like westerlies following afterwards, but Mr Duncan said it was still too early to confirm, with the weather so unsettled around the country.
The heavy weekend rain caused a section of State Highway 10 in Northland to subside and the NZ Transport Agency advised drivers that extreme care was needed.
The highway has subsided just north of the Matauri Bay intersection near Kaeo leaving just one lane for traffic to use.
The NZTA was installing temporary traffic signals to help drivers get round the slip safely.
"This section of highway is very narrow, and all drivers should use it with extreme care - especially at night," said NZTA spokesman Steve Mutton.