The total overtime cost has ballooned over the past two months from $17 million in March to nearly double that on Thursday, Kelly said at a City Council budget hearing.
The spike in spending follows the massive May Day protests of Tuesday, May 1.
The Occupy Wall Street protests — along with Hurricane Irene, which cost the NYPD $7 million in overtime pay — have busted the NYPD's overtime budget, pushing it up to $604 million for the fiscal year ending June 30, Kelly said.
That's $53 million more in police overtime than the city paid the previous year, he said.
While the NYPD is devoting a large amount of manpower to policing the protesters, Kelly said the effort is not hurting the NYPD's ability to fight crime across the city, since the overtime workers are taking on extra shifts on their days off.
"Most of these events, for instance Occupy Wall Street, that's covered by overtime," Kelly said. "So that's somebody who is not normally working. We’re not taking them out of the precinct. We’re having them work on their day off to cover these events. So the impact on commands…is minimal."
Kelly also blamed the huge rise in overtime costs on the city's cuts to civilian officers, whom the department uses for administrative duties so uniformed cops can spend more time on their beats.
The number of full-time civilian positions at the NYPD has fallen to 14,431, he said, and will drop to 14,107 next year.
"These civilian reductions have affected all department functions, especially clerical and administrative, and the city’s continued hiring freeze had limited the department’s ability to fill vacancies in technology, trade and other professional titles,” Kelly said in his testimony.
“It certainly has the potential of impacting adversely on patrols,” he added later during a question-and-answer session.
However, Kelly added that after years of declining ranks, the NYPD has just completed two major hiring rounds for uniformed officers, welcoming a class of 1,631 recruits between last December and this July and another 1,055 in January 2013.
While crime has edged up across the city so far this year, Kelly pointed out that murders are down, with 132 so far this year, compared to 168 by this time last year.
Queens City Councilman Peter Vallone Jr., who chairs the Council's Public Safety Committee, said he is still concerned there are not enough police officers on the force, but he called the murder decline "truly remarkable."