The two abortion clinics involved in the case say the state has no right to such personal information and are fighting the request in the Kansas Supreme Court.
"When a 10-, 11- or 12-year-old child is pregnant, under Kansas law, that child has been raped, and as the state's chief law enforcement official, it is my obligation to investigate child rape," Attorney General Phill Kline said.
Sex involving someone under 16 is illegal in Kansas, and it is illegal in the state for doctors to perform an abortion after 22 weeks unless there is reason to believe it is needed to protect the mother's health.
Kline spoke to reporters after details of the secret investigation, which began in October, surfaced in a legal brief filed by attorneys for the two clinics. The clinics argued that unless the high court intervenes, women who obtained abortions could find government agents knocking at their door.
The clinics said Kline demanded their complete, unedited medical records for women and girls who sought abortions at least 22 weeks into their pregnancies in 2003. Court papers did not identify the clinics.
The records sought the patients' "sexual history, birth control practices, prior medical and personal history, notes from the physical examinations, and a number of other things that the clinics contend are protected by the patient-physician privilege," Kansas Supreme Court spokesman Ron Keiffover told CBS Radio News.
The clinics are offering to provide records with some key information, including names, edited out.
"These women's rights will be sacrificed if this fishing expedition is not halted or narrowed," the clinics said in court papers.
On Oct. 21, state District Judge Richard Anderson ruled that Kline could have the files. The clinics then filed an appeal with the high court. No hearing has been scheduled.
The clinics outlined their legal arguments in a brief filed Tuesday. Though other documents in the case remain sealed, the brief filed Tuesday was not, and The Wichita Eagle disclosed Kline's investigation in a story published Thursday.
In their brief, the clinics' attorneys said a gag order prevents the clinics from even disclosing to patients that their records are being sought. Attorneys declined to comment Thursday, citing the order.
"You can see our desire to discuss as much as possible, but we feel constrained," said attorney Lee Thompson.
Thompson declined to say if his client was Dr. George Tiller, whose Wichita clinic is known as a provider of late-term abortions and is a frequent target of abortion opponents.
Kline would not discuss the scope of the investigation. Recently, Kline's office helped Texas authorities gather information from Tiller regarding a pregnant teenager who sought his care and died in Kansas.
Kline in 2003 began pushing to require health care professionals to report underage sexual activity. Kline contends state law requires such reporting, but a federal judge blocked him. The case has yet to be resolved.