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The chief executive officer of Waterfront Toronto, who has been spearheading a controversial plan to have Google-affiliate Sidewalk Labs build a futuristic community on the city’s lakeshore, is leaving his post.

Waterfront Toronto, a development agency with a board appointed by the federal, provincial and municipal governments, announced late Wednesday that earlier the same day Will Fleissig had told the board he was stepping down as CEO.

In an interview, Helen Burstyn, the chairwoman of Waterfront Toronto’s board, praised Mr. Fleissig and said the organization will need a new leader to concentrate “on flawless and relentless execution of some very important projects,” such as the Sidewalk Toronto partnership.

“[Mr. Fleissig] was a part of those discussions, and this was a resignation on his part,” she said. “It was a recognition … that this was perhaps a time for a change in focus to implementation.”

Two sources familiar with the negotiations said the departure was not a sign that talks with Sidewalk Labs over its ambitious plans to test new “smart city” technologies on the waterfront were in trouble. Ms. Burstyn said that Waterfront Toronto continues to work on signing a development agreement with Sidewalk Labs. That process “is going very well, and it’s looking like it’s going to work,” Ms. Burstyn said. “We’re very optimistic.”

Sidewalk Labs, owned by Google parent Alphabet Inc., said late last month it expected that the plan it is developing with Waterfront Toronto would not be finalized until next year, to allow for additional public consultation.

Mr. Fleissig could not be immediately reached for comment. Waterfront Toronto did not say why he was leaving. A former San Francisco developer and city planner in Denver and Boulder, Colo., he joined Waterfront Toronto in 2015.

The chairwoman said board member Michael Nobrega, a former president and CEO of the massive OMERS pension fund, will step in as acting CEO.

Ms. Burstyn added that herself, Mr. Nobrega, and chief development officer Meg Davis would take over while Waterfront Toronto searched for a new CEO.

Toronto Mayor John Tory praised Mr. Fleissig for his contribution and noted the importance of the company’s massive and complex project under way to protect the Port Lands from flooding, as well as the Sidewalk Labs initiative.

“Will Fleissig brought a great deal of vision and excitement to Waterfront Toronto, and I thank him for his work and wish him luck in the next chapter of his career,” Mr. Tory said in an e-mail.

Sidewalk Labs CEO Dan Doctoroff also issued a statement praising Mr. Fleissig and welcoming Mr. Nobrega.

The company was selected from a group of other bidders last year. Critics have raised concerns over how the data collected from sensors of cameras Sidewalk Labs has said it might install would be governed.

Some on Toronto’s city council raised concerns about secrecy around Waterfront Toronto’s initial agreement with Sidewalk Labs, which has not been released.

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