Floating warning sign buoys were also put into the water about midday to help make the closure more visible for beach-goers.
Bay of Plenty Regional Harbourmaster Peter Buell said the contaminants in the water appeared to be bilge oils, a mixture of different hydrocarbon products used in vessels, with a possibility that sewage had entered the water as well.
The Bay of Plenty Regional Council was alerted by the Port of Tauranga, just before 5am yesterday, that a fishing vessel could have leaked a mixture of contaminants into the harbour after a hole was found in the hull.
The tank that appeared to be the problem contained the vessel's sewage and was emptied into a sucker truck.
The quick clean-up action of the council meant the spill was contained by booms and collected effectively, he said.
The hull of the commercial fishing boat had been patched to stop the leak and, because the clean up got under way so quickly, there were limited concerns for wildlife in the area being affected, he said.
Tauranga City Council communications advisor Marcel Currin said water quality tests had been taken along Pilot Bay, Sandy Bay and Harbour Bridge Marina. The results came back clear this morning.
"The level of wastewater that entered the harbour remains unknown," he said yesterday afternoon.
Pilot Bay beach was closed to swimming as a precautionary measure with the closure being reviewed as more details became available, he said.
Mr Currin said the council wanted to stress the closure of the beach was a precautionary closure.
"The beach was closed on a 'better safe than sorry' basis. There was an outgoing tide at the time which will have helped disperse whatever entered the water.
"We are hopeful that everything will be clear for Christmas Day, but test results will give us more certainty."
Local beach-goer Hayley Hikairo was not impressed with the news.
"If it's contaminated there should be flags up, as there are children around."
Nevan Lancaster, owner of Mount Cats and Yaks, said the spill did not seem too bad.
"I went for a swim there this morning and there was a bit of a sheen.
"People are swimming around Pilot Bay at the moment [10.15am]. I don't think it's a major issue," he said.
An investigation into the source of the spill continued yesterday and will determine if the spill did originate from the commercial fishing vessel.
The boat had been detained by Maritime New Zealand and was pending repairs and inspection yesterday afternoon.