The closure comes on the back of an independent audit commissioned by the council and agency.
The audit came after a story in Bay of Plenty Times in July highlighting cyclists' fears for their safety. Read more here.
Tauranga city councillor Rick Curach, who is chairman of the city's Transport Committee, said he was aware of the safety concerns but "we weren't aware of the degree of safety until we eyeballed it ourselves".
Curach and councillor Bill Grainger, who represents the Te Papa/Welcome Bay ward, spent an hour at the cycleway junction yesterday. Grainger said he was concerned the closure of the road would result in recreating congestion along Welcome Bay Rd - an issue which has previously plagued the suburb.
"With that, you are going to have all the nose-to-tail traffic running back up to the Welcome Bay shops again."
The councillors said they preferred extending the existing cycleway into Welcome Bay Lane further and creating a turning bay and crossing point before rejoining the lane to the road ahead of the underpass.
Grainger said safety had to be the number one priority "but so is making sure that our options are going to be good for drivers and cyclists".
The audit found motorists were still travelling at speed despite interim safety measures such as lower speed limits.
The final design, timing and cost of these initiatives were still being confirmed.
In a written statement, transport agency project manager John McCarthy said the intersection met the current engineering code but "transport is changing and people should be able to safely use whatever mode of transport they prefer".
"We expect these changes will help to make cycling more attractive through the Welcome Bay area, which will, in turn, have a positive impact on everyone's travel times," Mr McCarthy said.
The Bay of Plenty Times sought comment from Tauranga City Council.
What's the problem
Welcome Bay Lane used to be the original Welcome Bay Rd leading up to the Hairini roundabout. However, when Welcome Bay Rd was diverted as part of the Maungatapu Underpass project, part of the road became a free turn and slip lane for westbound traffic. A green painted cycle lane cuts across the entrance to Welcome Bay Lane.
