Toronto chief planner Jen Keesmaat is calling for the removal of the eastern Gardiner, putting her at odds with the mayor on one of the most important issues facing the city.

"This is a decision that needs to be made by looking into the future and thinking about the kind of city we want to be in the future," she said Friday. ‎"We have an opportunity to create a grand new landscape in our city."

Ms. Keesmaat made clear her position at a conference hosted by the Cultural Landscape Foundation. It emerged in an onstage conversation with former chief planner Paul Bedford, who is also in favour of removing the Gardiner east of Jarvis.

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Mayor John Tory has spoken strongly for keeping the eastern Gardiner as an elevated highway. He says the expense of doing so – which will cost about twice as much, over the long term, as removing it – is a reasonable price to pay to avoid slowing some drivers.

The choice about the eastern end is being forced by the age of the elevated expressway, which is deteriorating. What to do with it is a decision that will ‎shape the eastern downtown for decades to come. It's the biggest issue to be weighed by council so far this term.

"We're at a moment right now that is a seminal moment," Ms. Keesmaat said during the conference. "A decision needs to be made."

The decision over the eastern stretch – with a price tag that could range up to close to $1-billion – is set to come to council in early June. And until Ms. Keesmaat spoke up it was looking as though council would make the decision without a clear opinion from senior city staff.

Tanzeel Merchant, executive director of the Ryerson City Building Institute, worries that there is a growing trend of civil servants keeping quiet.

"There is a tendency, across the board, for staff to say less and less, fearing recrimination," he said. "But I think it's a dangerous precedent because evidence-based policy is essential to making good decisions."

There are two options currently on the table: replacing the elevated Gardiner east of Jarvis with a street-level boulevard or re-building it in the same place, with some adaptation to the ramps.

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Replacing the elevated roadway with a boulevard will cost $461-million to build and maintain over its life, while keeping it – an option dubbed the hybrid – will cost $919-million over the same period. Removing it will free up more land for development but will mean delays of a few minutes for a small group of drivers, according to the city's environmental assessment.

Ms. Keesmaat said after her onstage remarks that she was professionally obliged to speak up for what she believes is in the best interests of the city.

"From an official-plan policy perspective, from our secondary-plan perspective for the waterfront, which focuses on making connections and complete communities and removing barriers, the policy framework that has been firmly established, and that in city planning we are responsible for implementing, very clearly leads to this conclusion," she told The Globe and Mail.

Mr. Tory said that Ms. Keesmaat is "perfectly entitled" to her views in her role as chief planner, but reiterated his support for rebuilding the elevated highway.

"I made a difficult decision but one that I think is right overall for that balance between the economy of the city, the ability of people to get around, and the ability to develop lands both here right on the waterfront, and nearby the waterfront," he said at an unrelated press conference on Queens Quay Friday.

"We're going to have a debate, and we'll hear from lots of people, and we'll make a decision. But I've sort of set out my own position. She's set out hers."

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Mr. Bedford, the former chief planner, said such differences of opinions were standard when he was in the role. "I disagreed with the mayors of the day on all kinds of issues," he said. "That's your professional obligation to say what you think."

One year ‎ago, city staff recommended taking down the eastern Gardiner. After taking time to study yet another option, this month they presented a report that didn't make a recommendation.

That report was followed by a meeting of the key Public Works and Infrastructure committee. After a full day of debate and discussion, it opted not to take a position, punting the decision ‎to the full council next month.

With a report from Ann Hui