Municipalities will be left to pay the entire cost of road repair on sections of some of Ontario's most critical highways now that the province has ended a long-running subsidy.

In January, Minister of Transportation Bob Chiarelli informed several municipalities that the province killed the Connecting Links Program.

The program was a subsidy that municipalities used to help fund construction, maintenance and repairs on roads the province designated as "connecting links," which are portions of provincial highways that run through communities and are not owned by the Ministry of Transportation.

In Windsor, Ont., for example, it means the city will now pay for all work on Huron Church Road, which links Highway 401 and Highway 3 with the Ambassador Bridge, North America's busiest border crossing and a key to economic trade with the United States.

The city estimates it costs $750,000 a year to maintain that stretch of road..

Manager of contracts Mark Winterton said he got the official cancellation notice a couple of months ago.

He called the program "spotty" at times, but in some years the city received as much as $500,000 from the government.

"That road is going to take a higher maintenance requirement than a local road," Winterton said of Huron Church Road.

Winterton said the decision to end the program took him by surprise and that municipalities were not consulted

"We hadn't got money [the last couple of years] so it looked like it was going away in advance," Winterton said. "They decided the program was going to be folded into other funding formulas."

The ministry confirmed to CBC News the Connecting Links Program has been cancelled. It's being rolled into the Municipal Infrastructure Investment Initiative or MIII.

"Through MIII, Ontario is providing almost $100 million over the next three years to help municipalities prepare asset management plans and address critical infrastructure projects," spokesperson Emna Dhahak wrote in an email to CBC News.

Dhahak didn't say how much the Connecting Links Program was worth.

Politicians across the province have been taken aback by the government's decision.

West Perth Mayor Walter McKenzie said the new funding falls short.

In a letter to Chiarelli, he said the MIII "would provide only a small fraction of the required funding" needed to maintain roads and bridges in his municipality.

Conservative MPP Randy Pettapiece said in a letter to Chiarelli that "it is difficult to understand ... why the government has offered nothing for shared infrastructure upkeep."

"This concerns an area where the province has, at least in part, traditionally assumed responsibility."