The contamination - and patches of slick that developed nearby - was then removed from the surface with skimming equipment on the NRC's purpose-built barge Taranui.
Disposable booms, designed to catch oil, were also floated around sludge the incoming tide carried on to the shore.
But, by midday, there was a wide, ugly black streak left at the high-tide mark along several hundreds of metres on the beaches' white sands.
Dozens of overall-clad workers used blotting equipment, diggers and spades to scrape up contaminated sand and they literally hand washed rocks at the marina entry.
Meanwhile, another skimming operation took place off Snake Bank, near the harbour channel, clearing up patches of oil being carried in that direction on the outgoing tide.
The clean-up was practically complete by late afternoon, incident controller NRC harbourmaster Jim Lyle said.
While the spill's origin was still under investigation by NRC and Maritime New Zealand staff last night, the primary focus yesterday had been on containing the oil and protecting the environment.
Attempts to recover smaller patches from the water were ongoing and it was expected more oil which had found its way ashore would be cleaned up before the overnight high tide.
Officials had no confirmed reports of wildlife being affected by the spill, although bird recovery experts were part of the response, as a precaution.
Mr Lyle said it is too early to say what - if any - enforcement action might be taken in the wake of the incident.
"Again, at this stage, our current focus is on containment and recovery."
Northport confirmed the Ningpo was officially identified as the source of the leak and her owners were flying a technical team from Singapore to investigate how it occurred.
Work on cleaning the hull and tanks, as ordered by Maritime New Zealand, was under way last night.
The smooth operation to clean up a real-life spill came only a day after the port and refinery specialist teams had undergone a training exercise.
"If anything good can be said about what happened today, it's that all the agencies and organisations involved in the use and management of Whangarei Harbour came together well to fix what happened in double-quick time," said Jon Moore, chief executive of Northport Ltd.
"The effectiveness of the team response was testament to the many hours of practice and preparation for just such an event. We are beyond grateful to everyone involved in the clean-up."