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The agency's principal transport planner Mark Haseley said the toll points would capture traffic coming from the interchange and on to the highway heading west towards Tauranga or Mount Maunganui.
Eastbound traffic would continue to be recorded by the existing toll gantry at the eastern end of the link.
Haseley said it was only fair.
"To ensure fairness for all users of the Tauranga Eastern Link toll road, people travelling via any proposed interchange should pay for their trip."
Noone would be tolled twice for the same trip, he said.
The tolls - $2 per car and $5 per truck - have been in place since the road opened in 2015, and the money collected goes towards repaying the $455 million cost of the road.
Haseley said there was more work to be done to confirm how the new tolling points would be implemented in detail without "adversely impacting growth in the area".
The agency was working with the council to bring the Papamoa East interchange forward from its current expected completion date of 2025.
It's not going to alleviate the traffic pressure on those local roads.
Papamoa East resident Jeremy Cunningham said tolling people heading to Tauranga from the Papamoa East Interchange would be "daft".
While the interchange was "long overdue", he did not see the benefit of a new tolling point when people would be able to take Te Okuroa Drive - currently being extended towards Golden Sands - or Papamoa Beach Rd for free.
"It's not going to alleviate the traffic pressure on those local roads."
He wanted more clarity from Tauranga City Council and the agency about the future of the interchange, and the tolling plans.
The agency's tolling plan was revealed in a business case for the council's application for a $60 million interest-free loan from the Government's $1 billion Housing Infrastructure Fund for infrastructure in Papamoa East.
Of that $60m, $39m would be put towards the interchange and nearby local roads, according to a report by council staff.
The council is also seeking $11.1m in cost-sharing from the New Zealand Transport Agency towards the interchange.
The Western Bay district has two of New Zealand's three toll roads: Route K (Takitimu Drive) and the Tauranga Eastern Link.
The agency has also previously considered tolling the planned Tauranga Northern Link, though the future of that project is unclear.