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Tensions ran high as Nash & Ross staff began taking sand off Tomahawk Beach for commercial purposes and flood protection about 7am yesterday.
Others were drawn to the beach after a heated exchange between Nash & Ross workers and members of the public.
Nash & Ross managing director Steve Ross disagreed with claims his crew scared the sea lion off the beach before work resumed yesterday.
The consent for the work he held did not refer to wildlife, but referred to public safety along with a host of other conditions, all of which were met, he said.
"The members of the public were acting illegally.
"We’ll have the police there next time they try something stupid like that," Mr Ross said.
"I’ve got as much time for wildlife as anybody, but what they were doing was absolutely bloody ridiculous."
The beach was sited off a sewage outlet, and there was a toxic algal bloom in the estuary signposted on the beach that would have been more of a risk to the marine mammal, he said.
Several members of the public described hearing howls of a sea lion over the noise of heavy machinery.
None reported seeing the pup.
Kim Gotlieb, who lives near the beach, said she was "over it".
"It’s abhorrent that the extraction of sand has priority over the protection of wildlife," she said
The incident yesterday morning was avoidable, New Zealand Sea Lion Trust chairwoman Jordana Whyte said.
"This whole incident has been really upsetting, to the sea lions first and foremost, and to the locals," Miss Whyte said.
The sea lion and pup were believed to be the pair that forced the closure of John Wilson Ocean Dr last month, she said.
Police did not attend the incident yesterday, a police spokeswoman confirmed.
Doc coastal Otago operations manager Annie Wallace said staff who attended yesterday advised the contractors to stop work when animals were closer than 50m or appeared otherwise distressed.
A mother and pup are known to be residing in the area, Ms Wallace said.
At this stage in the breeding season, the pups were getting older, and mothers did leave them on their own while they foraged at sea, she said.
Otago Regional Council compliance manager Tami Sargeant said the work was compliant with consent conditions.
The council and company were working together to install signage that outlined the purpose of the consents and their conditions.
The council was notified the work would go ahead yesterday on Wednesday, she said.