Auckland City wants a large ventilation building proposed for the southern end of the Waterview motorway tunnels to be buried instead of being allowed to loom over parkland.

"The large industrial-scale bulk of this building will have a major impact even next to a motorway," the city council has told the Environmental Protection Authority in a submission on the Transport Agency's $1.75 billion Waterview Connection project, which will extend from New Windsor to Te Atatu and to St Lukes.

Ventilation buildings with emissions stacks 25m high are proposed for both ends of a pair of tunnels running 2.4km from Alan Wood Reserve in Owairaka to an interchange between the Southwestern and Northwestern motorways at Waterview.

The council wants the northern stack built as far away as "practicable" from Waterview Primary School and a kindergarten, but has not asked for an associated control building to be buried.

Although the Transport Agency wants to build the stack beside Great North Rd, only 45m from the school and even closer to the kindergarten, it says the height means vehicle emissions will be dispersed widely into the atmosphere and will not need filtering.

But the council submission says the visual prominence of the stack and community perceptions of the effects of emissions could hamper greater residential development and the viability of the school and kindergarten.

Community groups say they will present evidence to a board of inquiry hearing in February that pollution would fall on the school on still and foggy days.

The Transport Agency says existing filtration technology does not offer enough benefits to justify an extra cost of about $70 million to install it.

Unlike the ventilation building in Alan Wood Reserve, a control house at the northern end of the tunnels will be staffed and the agency always intended to it to be about 6m high.

But Owairaka residents are shocked that the agency has withdrawn a plan to bury the 108m southern building, deciding instead to erect it 8m above what will be left of the reserve after a section of surface motorway runs through it from Richardson Rd.

The agency says not burying the building will save it about $5 million and give emergency operational advantages.

Bollard Ave resident Ora Emslie, whose home overlooks the reserve, has in a submission accused the agency of an "enormous departure" from what was earlier agreed through public consultation.

She said many people still assumed the building would be buried.

But the change would turn green space "into an industrial wasteland inviting criminal activity and tagging, reducing safety and quality of life for residents and homeowners."

The city council submission says little enough of Alan Wood Reserve would be retained even with the building buried.

Although the submission supports the project in principle as giving significant transport and economic benefits, it seeks more mitigation than that offered by the agency, which includes only one footbridge over the motorway corridor - in Hendon Park to the east of the tunnels - and extending its State Highway 20 cycleway beside only the 1.8km surface section of the new motorway.

"The [agency's] objective to support mobility and modal choices within the Auckland region is fundamentally undermined by omitting cycleways and pedestrian bridges above the tunnelled section of the corridor," the submission says.

* Alan Wood Reserve, Owairaka.

* Includes a 25m high emissions venting stack and will be 108m long.

* Northern control centre.

* Great North Rd, next to Waterview Primary School.

* Includes a 25m venting stack and will be 93m long.