One of two containers spotted in the swollen Buller River on Tuesday remains missing, officials say.
Police were stationed at numerous spots up the Buller Gorge on Tuesday night, with concern the containers could damage bridges.
Footage of one of the containers stuck under the bridge was posted to social media on Tuesday evening.
"So there is a fair bit of rain going on all over, with slips reported on a number of roads as well as flooding," Murchison Information Centre said on Facebook. "Someone has lost a blue container!"
Buller's Emergency Management officer says one of the containers is still wedged in a bridge, while the other is still unaccounted for.
On Tuesday night, people were asked to refrain from walking on bridges over the Buller River.
Further south, efforts are continuing to prevent Wānaka businesses from flooding as the storm continues to hit the South Island.
Water levels are rising in lakes Wakatipu and Wanaka and sandbags are on standby for waterfront businesses.
The Queenstown District Lakes Council (QLDC) said in a statement that locals are advised to keep monitoring lake levels.
"QLDC is making sand and 1000 25kg sandbags available in the Wānaka CBD and these resources are available from the Dunmore St car park and anyone wishing to use them will need to come along with a shovel and the means to transport safely back to their property," the council said.
Road speeds in the town's central business district have also been reduced to 30kmh.
"Currently, the QLDC emergency management team continues to monitor levels for Lake Wakatipu and is assessing the need for a similar precautionary measure of issuing sandbags for other potentially at risk areas," the council said.
A heavy rain warning remains in place for the headwaters of the Otago lakes and rivers, with additional warnings likely to be issued later on Wednesday.
Residents have been told to expect between another 60 and 80mm to accumulate on top of what has already fallen.
"Further periods of heavy rain are expected for the rest of the week," MetService says.
Heavy rain warnings also remain in place for Fiordland, Westland and parts of Canterbury.