Critics have said the sound, occurring every five seconds over 30 days, could directly harm fish - and, by extension, the recreational and commercial fishing industries, plus tourism - and could disrupt migration patterns of whales and other marine mammals.
It also said endangered species could be affected.
"We must carefully safeguard those resources, which play such a key role in our state's $40 billion tourism industry, for the benefit of our residents, businesses, and the environment," state Environmental Protection Commissioner Bob Martin said.
"The Christie administration continues to focus on clean ocean water quality, protecting our coastline, and working to enhance our coastal recreation and fishing industries," he said.
The legal action names the foundation, which is funding the research; the National Oceanic and Atmospheric Administration, which denied a state request to review the project; and the Lamont-Doherty Earth Observatory in Palisades, N.Y., which operates the vessel.
The research project is being led by Rutgers University geologist Gregory Mountain. The ship is at sea with researchers aboard, preparing for the study.
A DEP spokesman said officials expected court action Monday.
The DEP said the study's one-month time window coincided with the height of fish migrations. It also is when about 20 percent of the annual catch for many species occurs.
"We have made our concerns clear to the NOAA and remain hopeful that, at the very least, this initiative will be rescheduled for a less-impactful time of year," Martin added.
The state had sought permission from NOAA to review the project, saying it had the authority to do so under the Coastal Zone Management Act. NOAA officials denied the request, saying it had not been filed in a timely manner. The DEP contends the denial was improper.
Earlier, the DEP submitted a document arguing that the National Marine Fisheries Service should not approve a permit for a "take" - or harming - of marine species.
The service later issued the permit and said that while some species might be disturbed, none was expected to die as a result of the testing.
However, the DEP noted that the foundation's environmental study of the project concluded that limited knowledge of the effects of seismic surveys on marine fish "makes drawing conclusions about impacts to fish problematic."
Part of the study area, which is a rectangular grid that begins about 15 miles southeast of Barnegat Inlet, includes areas identified as essential fish habitat, the DEP said, which are important for spawning, breeding, and feeding.
The DEP said that the sound levels of the pulses could reach 250 decibels underwater and that "the threshold level where underwater noise is considered to pose dangers to marine wildlife is 160 decibels, which is louder than a jet engine."