The Murphy administration on Wednesday night denied three key permits for a controversial pipeline that would send natural gas from New Jersey under Raritan Bay to New York City.

The state Department of Environmental Protection's denial of the 24-mile underwater Northeast Supply Enhancement pipeline proposed by energy company Williams follows a similar rejection by New York regulators last month.

A Williams spokesman said Thursday morning that the company will resubmit its application, echoing what the company said after the New York denial.

"We believe that we can be responsive to the issues raised by the agency and intend to resubmit the application to the agency in a timely manner to maintain the customer’s in-service date requirement," said Chris Stockton, a Williams spokesman.

Along with the Raritan Bay portion of the pipeline, the DEP denied approval for a 6-mile pipeline in Sayreville and Old Bridge in Middlesex County and a key compressor station in Somerset County that make up the NESE project.

The project — an extension of the Transco pipeline — was seen as a key transporter of fracked Pennsylvania shale gas to New York and the Northeast.

In its 15-page denial, DEP officials rejected the Raritan Bay portion of the pipeline saying dredging could "adversely impact surface water quality."

"Transco has not fully demonstrated how it would avoid or minimize adverse impacts to surface water quality," the DEP said in a statement released late Wednesday.

Similarly, the DEP said the company has not shown "alternatives that further avoid or minimize impacts to freshwater wetlands and riparian areas" for the 32,000-horsepower, gas-fired compressor station slated for Franklin in Somerset County.

The denial was met with applause from several New Jersey environmental groups, many of which held rallies against the pipeline proposal. Opponents said the pipeline would harm the bay and the communities it would run through. They also said it would be a blow to Gov. Phil Murphy's clean energy goals.

"If we are serious about confronting climate change, these fossil fuel projects simply cannot be built," said Junior Romero, an organizer with the advocacy group Food & Water Watch. "Governor Murphy should seize this moment to go further, by calling for an immediate moratorium on all new fossil fuel projects in the state."

Business and labor groups have lobbied in favor of the pipeline, saying investment in job creation requires certainty about a sufficient energy supply.

The pipeline is opposed by Middlesex County and officials from several municipalities. It was approved by the Federal Energy Regulatory Commission on May 3.

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