Water samples collected by the U.S. Environmental Protection Agency showed no indication of "red tide" or other toxic phytoplankton, the state said.
The DEP is also analyzing oxygen levels in the water.
"Right now, we just don't know" what caused the die-off, said DEP spokesman Larry Hajna. "It's a mystery."
Budd, a commercial crabber and owner of Budd's Bait & Tackle in Villas, said there were millions upon millions of bunker in the bay.
"If you're on my boat when we're working, the bunker are jumping all over. Sometimes the water is wrinkled with them," he said.
Eric Stiles, vice president for conservation and stewardship of New Jersey Audubon, said he had never heard of such a massive die-off of menhaden. They are a "critical fish" in the ecology of the bay, he said, so the fish kill is likely "highly significant."
DEP conservation officers are working with the Cape May County Office of Emergency Management to evaluate the beaches.
The area is marshy and largely inaccessible from land, so the DEP also dispatched an aircraft to better assess the extent of the die-off.
Contact staff writer Sandy Bauers at 215-854-5147 or sbauers@phillynews.com Visit her blog at http://go.philly.com/greenspace.