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Toronto city manager Joe Pennachetti has written to the federal government, asking for funds to help build a Scarborough subway.Kevin Van Paassen/The Globe and Mail

Toronto has put in writing its $660-million request to the federal government to help build a Scarborough subway, even as it continues to wrestle with the province over the route the line would take and who would pay if it goes over budget.

City manager Joe Pennachetti sent the letter to Ottawa Thursday morning, less than three weeks before a Sept. 30 council-imposed deadline to secure funds.

The deadline was one of several conditions council imposed in July when it endorsed a plan to replace the aging Scarborough rapid transit line with an extension of the Bloor-Danforth subway to Sheppard Avenue rather than light rail as planned. Since then, provincial Transportation Minister Glen Murray has proposed that the subway run on the existing transit right of way – an option TTC chair Karen Stintz dismissed.

"It's a Rubik's Cube that we have. It is complex," Mr. Pennachetti said Thursday before a meeting with the provincial transit agency, Metrolinx.

Mr. Pennachetti said city staff is involved in "very serious discussions" with both the provincial and federal government on possible subway funding. He and TTC chief executive Andy Byford expect to have a detailed report ready by Oct. 4, in time for a council meeting Oct. 8, he said.

"There could potentially be options for council's consideration as we all know depending on what we hear from the federal government and the provincial government," he said.

Whatever the outcome of those discussions, Toronto Mayor Rob Ford insisted the city will not be on the hook for additional costs. "The message is we are not paying for any overruns," he said Thursday at a lunchtime news conference to highlight the city's economic health.

During Question Period at Queen's Park, Premier Kathleen Wynne said her government will keep its commitment to build a subway in Scarborough with $1.4-million and using the route Mr. Murray proposed.

Ms Wynne said she made that point during a meeting Wednesday with Ms. Stintz, but also suggested her government might be open to a change if federal funds are available.

"I said to Councillor Stintz, if she can find a way to bring that money forward, then that's one thing. But the fact is that money has not been forthcoming." Ms. Wynne said.

Doug Holyday, Toronto's former deputy mayor and now a Progressive Conservative MPP, criticized the Transportation Minister for adding to the confusion over Toronto's transit plans. "Every time he opens his mouth, he either insults someone or releases a new plan," he said in the legislature. "I wouldn't trust him to run a one-car funeral."