The Australian Medical Association NSW and the Asthma Foundation NSW are both concerned about health effects from the $3 billion NorthConnex tunnel connecting the M1 and M2, and have called on the government to ensure its approval is not rushed.

But the state government insists it would not be building the tunnel unless it was safe, and air quality will be stringently monitored.

One of the two ventilation stacks for the 9km tunnel is currently planned for its entrance at Wahroonga. Doctor and resident Ray Nassar said Knox Preparatory School and Abbotsleigh School for Girls were among 17 schools, pre-schools and childcare centres within a one kilometre radius of the stack, along with five aged care facilities and two hospitals.

"With children especially there are concerns that exposure to the pollution will cause permanent and irreversible damage to growing lungs," he said. "Our concern is not only about actually causing asthma and bronchitis, but also lung development, and, down the track, cancer.

"The pollution we will be showering people with is indisputably carcinogenic."

Dr Nassar said he was particularly concerned the stack was only 23 metres tall at its highest point. By comparison, the Cross City Tunnel ventilation stack is 65 metres high, he said.

In addition, modelling of the dispersal of air pollution used weather patterns from other parts of Sydney, including Terrey Hills, 20 kilometres away, and Sydney Airport.

"The weather they have assumed will cause a dispersal is not local at all," he said. "We have a lot of days where there is absolutely no wind, and that is going to have a major impact on the dispersal."

He is sending government ministers a petition signed by 250 doctors concerned about the pollution risks.

While pollution is known to be a major cause of death in Australia, killing nearly 1600 people in cities each year, claims ventilation stacks are directly responsible are controversial. Tunnel advocates claim they simply disperse existing pollution, and the environmental impact statement for NorthConnex has found it will have "negligible" effect on health.

However, a 2012 study which measured the lung function of hundreds of people living near the Lane Cove tunnel found those living near the ventilation stack experienced decreases in lung capacity and function.

Study author Christine Cowie, a senior research fellow at the Centre for Air Quality Health Research and Evaluation at the Woolcock Institute, said it was not clear the ventilation stacks were to blame.

Her research has also found being exposed to traffic on major uncovered roads can have significant health impacts, although residents living near the bypassed Epping Road did not experience health improvements after the tunnel was built.

"A lot of the other [research] seems to show beneficial effects of closing down roads and redistributing traffic and others have shown not much change," she said. "What is clear is that these similar projects will have very local effects".

AMA NSW president Saxon Smith said the government needed "to recognise that there is a health concern which is still being elucidated around ultra-fine particles [in traffic pollution]." The number of schools in the area was also concerning.

Asthma Foundation NSW CEO Michele Goldman said she thought the project was being rushed.

"We need to allow enough time to make sure that the environment and health assessments are done correctly," she said. "There is no safe level of exposure to some of the emissions from vehicles, and small particulate matter, ultra-fine particles, are of major concern."

The NorthConnex environmental impact statement is open for comment until September 12. Dr Nassar has organised a community forum for Thursday September 4, at 7pm at Barker College.

NSW Health said it was currently preparing a submission to the environmental impact statement, and so could not comment. NorthConnex referred Fairfax to Roads and Maritime Services, whose spokeswoman said: "We've carefully considered the issues surrounding the health of residents, carried out a comprehensive health risk assessment and the proposed design will ensure there will be no adverse impacts either to health or to local air quality."

"The proposed ventilation outlets for the NorthConnex tunnel are planned to be at least 40 to 50 metres from the closest residential property. This compares to between 10 and 25 metres from properties near the Eastern Distributor."