Communities in the path of Auckland's planned $1.7 billion Waterview Connection motorway project look set for at least a partial victory in their battle for tighter conditions.

A board of inquiry appointed by the Government to oversee a fast-track consenting process for the country's largest transport project has accepted their submissions on where vehicle emissions towers should be erected at each end of a pair of motorway tunnels.

The five-member board chaired by Environment Court Judge Laurie Newhook has directed the Transport Agency to build a northern tower on the other side of Great South Rd from Waterview Primary School, which is next to its preferred site.

It also wants a tower in Owairaka at the opposite end of the tunnels to be built 70 to 80 metres southeast of the agency's preferred site, away from a narrow chokepoint in Alan Wood Reserve.

That will mean a short extension to the 2.5km tunnels and was opposed by the Transport Agency, even though its own witnesses acknowledged that altering the location would reduce the project's displacement of scarce open space.

The board, which ended 16 days of public hearings in late March, has issued these and other directions ahead of a draft decision on the overall project due by the end of this month and a final verdict on June 30.

Other board directions include requiring the agency to pay $8 million towards a cycleway between Owairaka and Waterview.

The agency told the board during its hearings that $11 million to $21 million in extra costs spent on moving the location of the tunnels' southern ventilation building and partly burying an associated ventilation building could be better spent on other mitigation.

It estimated that building the northern emissions tower across Great North Rd from the primary school could add up to $29 million to the bill.

The board has, meanwhile, instructed the agency to build the two towers to a height of "15 metres above ground - not more - not less".

Mt Albert Labour MP David Shearer said he believed the directions, should they be adopted in full, would significantly lessen the motorway's impact on the local community.

* Includes 4.5km of new motorway - including a 2.5km pair of tunnels - from New Windsor to Waterview, connecting State Highways 20 and 16, to complete Auckland's 48km western ring route.
* Widening more than 8km of the Northwestern Motorway from St Lukes to Te Atatu.
* Expected completion date: End of 2016, with construction due to start before Christmas.