The next phase of the Second Avenue subway should be put on ice if the MTA doesn’t get the money it needs from the city, Chairman Thomas Prendergast said Monday.

Prendergast said the agency should reconfigure its capital plan — including cutting out the new subway line’s expansion from Harlem to the Financial District — if it doesn’t get the additional $3.2 billion it wants from the city for its budget.

The suggestion infuriated some board members, who said the board should instead look at all MTA projects across the region, and preferably nix one with less planned ridership.