The city is teaming up with the Port Authority on a $250 million project to help clear the way for new mega-ships to sail into New York Harbor once the Panama Canal is expanded next year.

To make way for deepening of the harbor’s channel, an old backup water-supply pipeline between Brooklyn and Staten Island must be ripped up and replaced with a new pipe deeper under the harbor, Mayor Bloomberg said.

“Thousands of miles from here they’re digging a new Panama Canal and we have no choice but to change the infrastructure here,” said the mayor. “If not, the ships just aren’t going to come here.”