A furious Christine Quinn yesterday said she has “zero tolerance” for City Councilman Dan Halloran’s flings with young staffers, as an ethics panel prepares to grill the proudly practicing pagan on his questionable relationships.

“Let me be clear: If these new allegations against Councilman Halloran are true, we will throw the book at him,” the council speaker stormed, just hours after she instructed the Standards and Ethics Committee to investigate Halloran.

Quinn ordered the probe after The Post exclusively reported that Halloran — already under federal indictment in the Sen. Malcolm Smith vote-rigging scandal — is shacking up with former council intern Denise Batista, 23, and previously bedded his former deputy chief-of-staff, Meaghan Mapes, then 21.

Both relationships began when the women were college students working in Halloran’s office, sources have said.

Batista and Mapes are expected to be called before the ethics panel and asked about their relationships with the Queens Republican, said a source familiar with the process.

Current and other ex-Halloran staffers also will likely be called in the probe, which could lead to his ouster from his $112,500-a-year council gig.

“One of the allegations [of an affair] I believe is [from] an intern, which is even more troubling,” Quinn said, answering questions about the probe after a press conference announcing an educational initiative at the Urban Institute of Mathematics in Throggs Neck.

“We have zero tolerance for sexual harassment and that type of behavior in the council. Just zero tolerance; we will not stand for it.”

Quinn said the ethics committee will open the matter “either on Wednesday or Thursday.” adding that the council’s legal team was told to “immediately begin an investigation.”

“If he did what is alleged,” she said, “We will use the full power of the council’s rules and the city’s work laws to punish him.”

Meanwhile, another former Halloran employee, Chief of Staff Chrissy Voskerichian, yesterday filed with the city’s Campaign Finance Board to run for his seat this fall, records show.

Halloran, who faces up to 45 years in jail if convicted, yesterday holed up in his Flushing home with Batista — where two federal agents paid him a visit, staying for about 15 minutes.

He declined to speak about the council ethics probe and the meeting with the feds, saying, “I hope you can appreciate that I can’t comment right now.’’

Additional reporting by David Seifman and Lorena Mongelli