The department is reducing staffing from five firefighters to four on 49 engine companies, which is the same staffing level on most engines throughout New York.
The department says the current labor contract with the Uniformed Firefighters Association calls for the reduction if the overall firefighter absentee rate exceeds 7.5 percent.
Firefighter medical leave rates reached 7.53 percent on Monday, FDNY said in a statement issued Monday.
According to the city, higher medical leave rates result in overtime expenses and approximately $20 million could be saved annually through the reduction.
"Medical leave rates have been rising for several months and we repeatedly warned the UFA this was a problem that could again result in the staffing reduction as outlined in their contract with the city," said Fire Commissioner Nicholas Scoppetta.
While the city says staffing reductions will not affect fire response times, UFA denounced the decision, saying it will endanger civilians and firefighters.
"It's going to take them twice as long to get water on the fire - of course that's impacting the safety of the public, the taxpayers and firefighters," Steve Cassidy, President of the UFA, said in a press conference. "They continue to mislead the public about response times."