Officials say the cuts represent the deepest one-year staff reduction in the agency's 30-year history.
"These are extremely painful steps, but unavoidable ones," NJT Executive Director James Weinstein said in a statement. "We must close our serious budget shortfall, and we at NJ Transit must do our part by making this the leanest, most efficient agency possible, without compromising safety."
A message left for the New Jersey local of the United Transportation Union was not immediately returned. The staff cuts will include both union and nonunion jobs, NJ Transit said.
The agency said the cuts will help whittle down a combined $300 million budget deficit projected through 2011 by about $30 million.
NJ Transit said it will also look to reduce costs for parts, fuel and utilities and to renegotiate contracts for some services.
New Jersey Gov. Chris Christie has frozen portions of NJ Transit's subsidies and called on the agency to improve its operating efficiency.
The riding public will be asked to bear some of the cost.
Weinstein said NJ Transit officials would announce proposals for fare and service changes next week.
"Unfortunately, fare and service changes will have to be a part of NJ Transit's overall response to this financial crisis," Weinstein said.
The agency last raised fares in 2007 by about 9 percent.