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Karen Stinz, TTC Chair and Toronto city councillor leans in to hear a journalist's question as she stands with Andy Byford, Chief Executive Officer of the Toronto Transit Commission while they scrum with reporters at City Hall in Toronto on Wednesday March 27, 2013.

The city councillor in charge of the Toronto Transit Commission is raising doubts about the province's authority to take control of transit construction in Scarborough, asking pointedly about a pre-existing agreement for a different project in the area.

In a sharp letter that raises a series of concerns about a new plan announced unexpectedly this week by Ontario Transportation Minister Glen Murray, TTC Chair Karen Stintz seeks "clarity" on costs and governance.

Ms. Stintz noted that the CEO of Metrolinx, the provincial agency that was intended to take the politics out of transit planning, had formally said at least twice this summer that a transit master agreement for the city was still in force.

The master agreement – signed by the city, TTC and Metrolinx -- specifies a light-rail line in Scarborough. Mr. Murray's surprise announcement that the province planned to go it alone on a subway extension in Scarborough involves laying the track on essentially the same route that had been designated for an LRT, meaning that it would have to supplant the earlier proposal.

"Of overriding importance is the current status of the Master Agreement," Ms. Stintz wrote in letter to Metrolinx chair Rob Prichard. "I request confirmation that this is still the case."

A spokeswoman for Metrolinx told The Globe Friday that they view the agreement as a legal contract that cannot be changed without the consent of all parties.

If consensus cannot be reached, the agreement seems likely to stand and an LRT would remain the officially agreed upon proposal.

Mr. Murray's subway proposal is the latest twist in a tortuous series of transit plans.

The Scarborough LRT was one of four new light-rail lines, all funded by the province, that were to be built in Toronto. Critics led by Toronto Mayor Rob Ford rejected the Scarborough line as not good enough and pushed for a subway. In the summer, Metrolinx said it would stop work on the LRT and seek clarity from the city. Council then approved a subway line that would be longer and run on a different route. Mr. Murray's plan returns to the original route but replaces the LRT with a short subway, saying that the province had been unable to get serious funding commitments from the city or federal government.

On Friday, though, local federal cabinet minister Lisa Raitt suggested that Mr. Murray was jumping the gun and that Toronto and Ontario need to sort out what they want and speak "with one voice."

"We need clear lines and we need clear direction," she told CP24. "We're trying to get a bead on where this is going. But we really need the province and the city to agree on [a] project, and what it looks like."

In her letter Friday on the latest proposal, Ms. Stintz also raises a series of other issues related to cost and governance.

She wants to know if the plan has been approved by the Metrolinx board and whether council's proposed subway is off the table, and with it any attempt to seek federal funding. As well, the letter seeks clarity on who would pay for any cost overruns and for shuttle buses during construction, as well as whether Metrolinx feels it needs to seek any approvals from the city.

Noting that the Metrolinx board is to meet next week, Ms. Stintz is seeking answers by Sept. 19.