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TALLAHASSEE (CBSMiami/NSF) —  Planned Parenthood is asking a judge for an emergency ruling after allegations three of their Florida clinics were performing second- trimester abortions without proper licensing.

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They are seeking an emergency injunction against the state Agency for Health Care Administration “to protect women’s access to safe, legal abortion.”

As grounds for the injunction, Planned Parenthood said AHCA was ignoring a 2006 agency rule, which defined the first trimester as “extending through the completion of 14 weeks of pregnancy as measured from the first day of the woman’s last menstrual period.”

Tallahassee attorney Julie Gallagher, who represents Planned Parenthood and is a former AHCA general counsel, said the agency had been conducting regular inspections and reading patient records and reports based on that definition since 2006.

“Nobody has ever deemed these procedures to be second trimester,” Gallagher said. “Suddenly, after nine years of using language that we agreed to in a rule challenge — and everybody’s been on the same page for nine years — suddenly they’re saying that these procedures that are performed and documented this way are now second-trimester procedures, and illegal at that. And we say, ‘No, they’re not.’ ”

The proposed injunction, filed in Leon County circuit court, follows Gov. Rick Scott’s order last month that AHCA investigate 16 Planned Parenthood offices that perform abortions to ensure they were following state laws. The order came as Planned Parenthood was under fire nationally following the release of a series of undercover videos by the pro-life group Center for Medical Progress, including footage that showed a Planned Parenthood doctor discussing the disposition of fetal tissue. During the controversy that ensued, Scott called the videos “deeply troubling” as he announced the investigation.

AHCA said last week that three Planned Parenthood clinics — in St. Petersburg, Fort Myers and Naples — were licensed to perform only first-trimester abortions but also performed some procedures in the second trimester.

The agency’s documents indicate that AHCA defined the start of the second trimester differently than the clinics. The clinics considered the first trimester to last 13 weeks and six days, while state investigators used a rule defining the second trimester as the “portion of a pregnancy following the 12th week and extending through the 24th week of gestation.” The documents said abortions were performed, for example, at 13 weeks and three days and 13 weeks and four days.

“If you look at the definition of second trimester and what they reported, in terms of number of weeks of gestational age — I’d go back to them and ask them what they reported,” AHCA Secretary Liz Dudek told reporters last week.

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The three clinics have been told “to immediately cease performing second trimester abortions,” an AHCA spokeswoman said earlier this month, and could face fines of up to $500 per violation.

Gallagher said the three clinics are the only Planned Parenthood facilities in Florida that aren’t licensed to perform second-trimester abortions; the others perform both. She said part of the reason for seeking the injunction was to protect the clinics and their staff members from facing further action, including potential criminal charges, although none has occurred to date.

Meanwhile, Gallagher said, the clinics have stopped performing abortions within the disputed date range.

“At our expense, we’ve taken to redirecting these patients to different facilities for services that they want and need,” she said. “It’s a great disruption to the daily operation of the facilities and also to the patients.”

She also said that a fourth Planned Parenthood clinic, in Pembroke Pines, cited by AHCA for improperly labeling fetal remains that were temporarily stored in a freezer, was in compliance with state law.

“That was an extra requirement, not mandated by Florida laws or rules,” Gallagher said. ”

Planned Parenthood has denounced the state’s allegations as politically motivated.

“Nearly a decade ago, state officials made it clear that Planned Parenthood is operating fully within the law, and nothing has changed,” Barbara Zdravecky, CEO of Planned Parenthood of Southwest and Central Florida, said in a statement. “The state’s actions are patently disingenuous and constitute a wholly unwarranted political attack.”

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(The News Service of Florida’s Margie Menzel contributed to this report.)