Chairman Marty Davis and kaiwhakahaere Anne-Marie Broughton said discharging wastewater to sea was contrary to the tribe's environmental management plan.
"Activities that involve discharge of contaminants, especially discharge of sewage, treated or untreated, lead to degradation of our waterways," the plan reads.
The problem was bigger than E. coli bacteria from faeces, Mr Davis said.
"There's heavy metals from commercial facilities. What's happening to all this stuff?"
The iwi supports further treatment of the waste and discharge to land.
"We need to look for alternatives and stop creating as much waste as we do," Ms Broughton said.
Sustainable Whanganui neither supported nor opposed the consent, board member Judith Timpany said. It wants to make sure the discharge is for a limited time, is monitored, and consent can be reviewed if circumstances change.
MidCentral District Health Board medical officer of health Patrick O'Connor supported the consent, because it gave the council time to look at alternatives. But he said the discharge did pose a risk to public health.
In calm sea and south wind conditions - 5-7 per cent of the time - the outfall plume gets within 300 metres of South Beach. At those times, faecal coliform numbers will be high, especially in the morning, and swimmers are at some risk of vomiting and diarrhoea illnesses.
He is recommending putting a sign at South Beach and information on Wanganui and Horizons council websites.
He was also concerned Wanganui District Council might not be considering all available treatment options - especially the option to treat industrial waste separately from domestic waste. He said that was done in Gisborne, Napier and Timaru.
Tasman Tanning and Cavalier Spinners, which contribute to the industrial waste load, support the consent as an interim measure.
Craig Thiele from Tasman Tanning said the company acknowledged its own contribution to improving the nature of its trade waste, to minimise the environmental effect of the discharge.
Wanganui District Council chief executive Kevin Ross said the council would be contacting all the submitters.