Judge Paul W. Clark dismissed the case against Tiller after Sedgwick County District Attorney Nola Foulston said that her office had not been consulted by Kline, a vocal opponent of abortion.
Clark signed his one-page order only hours after Kline's complaint against Tiller was unsealed.
Kline filed his complaint Thursday, alleging that Tiller had improperly performed late-term abortions and hadn't properly reported information to the state Department of Health and Environment.
Foulston said in her request to have the case dismissed that while Kline is the state's chief law enforcement official, he doesn't have the legal authority to "unilaterally" pursue criminal charges when a county prosecutor has not asked his office to intervene or granted a request from the attorney general to handle a case.
"The district attorney has not invited or requested, consented or acquiesced, or failed to object to the filing of the complaint," Foulston wrote.
She added: "The district attorney does in fact object to any such filing by the attorney general, as he lacks the legal authority to file such a complaint in this jurisdiction."
Foulston cited a law saying the attorney general "shall consult with and advise" county prosecutors "when requested by them" in "all matters pertaining to their official duties."
Tiller's clinic, known for being one of the few in the United States to do late-term procedures, has been a high-profile target of anti-abortion protesters for decades. The clinic was bombed in 1985, and Tiller was shot in both arms by a protester in 1993.
Kline, who lost his re-election bid in November and leaves office in three weeks, has been investigating whether Tiller and other abortion providers performed illegal late-term abortions in Kansas or failed to report suspected child abuse as required by law.
He waged a two-year legal battle before finally this year obtaining the records of 90 patients from Tiller's Wichita clinic and a clinic operated in Overland Park by Planned Parenthood of Kansas and Mid-Missouri.
Since the election, abortion rights activists have expected him to move against Tiller and perhaps Planned Parenthood as well.
When charges were unsealed Thursday, Tiller's attorney Dan Monnat said, "The filing of criminal charges by Phill Kline is the last gasp of a defeated and discredited politician," the attorney said. "Rather than executing his duty as a prosecutor to see that justice is done, he has chosen to engage in a malicious and spiteful prosecution on the eve of Christmas."