The move would restore subway service to the southern terminus of the No. 1 line for the first time since the storm flooded large portions of lower Manhattan Oct. 29. The work would include connections between the No. 1 train and the R train.

The move is not without problems. The old station features curved platforms far shorter than train lengths, both disrupting smooth passenger flows. The new station, which opened in 2009 and cost $545 million, eliminated those problems and improved connections not just between subway lines but also with the Staten Island ferry, which MTA also oversees.

They reconsidered, however, because of the agency's timeline for fully restoring South Ferry, said Thomas Prendergast, the chief of the MTA's transit division as well as the agency's interim executive director. MTA officials have said it could take as long as three years.

"It became clear that the time necessary to repair it would be too long a period to deny our customers a direct link to lower Manhattan," said MTA New York City Transit President Thomas F. Prendergast.

MTA will revamp the old station at an estimated cost of $2 million. Restoration of the replacement station is still being debated, with estimates running as high as $600 million.