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NEWARK, N.J. — New York and New Jersey announced Thursday how they will pay for their share of an estimated $13 billion project to build a new rail tunnel under the Hudson River and other improvements, with New Jersey’s outgoing governor outlining a plan that calls for progressively steeper fare hikes for train riders in his state during the next 20 years.

New Jersey’s Democratic Governor-elect Phil Murphy immediately took issue with the decision to raise fares.

‘‘I’d like to know whether there were alternatives that did not involve further fare hikes and if so why they were not pursued,’’ he said. ‘‘This is the type of deal that tells you a lot about why people are frustrated with politics. You wait until the last minute to take action, and then you settle for some deal that got cut in a back room somewhere so that one side or one politician or another gets a win without regard for the impact that it may have.’’

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The plans set up a framework for local funding of one-half of the cost of the tunnel and associated construction west of Penn Station in Manhattan.

ASSOCIATED PRESS