The Tararua District Council is seeking outside advice after another positive E.coli test has been returned for Pahiatua's water supply.

District mayor Roly Ellis said although people must continue to boil their water, the contamination is not in the town's water reticulation (pipe) system.

"This is so frustrating, especially after the high hopes we held after Sunday's clear test," Mr Ellis said.

"I went down to Pahiatua yesterday with Dave Watson, our utilities manager, and can assure people the Pahiatua bore is properly fenced, sealed and secure.

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It's very odd that we had a completely clear sample on Sunday, but another positive one yesterday, so that's why we're seeking outside help, just to confirm the actions we are taking are correct.

"We thank you for the positive way everyone is handling this."

Pahiatua residents must boil their water and continue to do so until three clear tests from water sampling have been returned.

The Pahiatua reticulation network continues to be tested at multiple sites.

Council said affected households and businesses may experience a discolouration of water or a strong smell of chlorine. "This is normal following extensive flushing of the reticulated system."

Anyone experiencing these issues is advised to run their taps for a few minutes until smell or discolouration lessens.

Mr Ellis earlier said he had no idea what had caused the problem at the bore.

This was the second time this year E.coli had been detected in a council water source. In early March, Pongaroa residents were issued with a boil water notice, after their urban and rural supply failed an E.coli test. The notice was lifted two weeks later.

Council's manager for district strategy and development Peter Wimsett said at the time the problem had been caused after the supply's chlorinator failed.

Council has secured funding from the Ministry of Health for up to $393,000 for the upgrade of Pongaroa's water supply, with an estimated cost of $150,000.