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McKeown Group managing director Ken McKeown said the tanks were removed on Wednesday morning as part of the company's compliance with an Otago Regional Council abatement notice, but "those tanks have proved not to be the problem".
"ORC are going to have to give us a reprieve from the abatement notice they gave us because we've removed the two tanks they wanted us to investigate and the samples have come up clear in the hole and there were no holes in the tanks," he said.
"So they pointed the finger at us - obviously because we're the only ones down here - but we've just taken the tanks out this morning and they're clearly not the source of the problem."
After the council investigated public complaints of a sheen covering several square metres of water in the harbour late last year and again early this year, the company was ordered to remove underground petroleum storage tanks, dispose of petroleum and impacted groundwater from within monitoring bores, mitigate any further contamination of the coastal marine area, and install warning signage at its Esplanade St site to warn the public of the potential presence of hydrocarbons.
Mr McKeown said yesterday the council "do need to redress it somehow".
"They've put it on us that we need to do this, this, and this. And we've complied with that."
He reiterated his view, which he first expressed when he spoke to the Otago Daily Times about the matter in September, that there were other possible sources of hydrocarbon contamination in the area due to the harbour's historic use.
In October last year, the excavation of a test patch at a neighbouring vacant waterfront property owned by the Waitaki District Council led to the council removing a small fuel tank at the site - a former Shell station - which was thought to be the source of the fuel.
But that did not fix the issue and in May investigations resumed.
Last week, ORC regulatory general manager Richard Saunders said the council was "comfortable with the progress that McKeown's are making in
complying with the issued abatement notice".
"We continue to monitor the situation and will follow up if required."
A council spokesman yesterday said it would "review any information that we receive from McKeown Group and respond accordingly".