Los Angeles Superior Court Judge Renee Korn said that she would have to free him soon, if charges aren't filed in a similar case in Louisiana.
"To hold him into perpetuity on an arrest warrant seems to be grotesquely unfair," Korn said.
Sharper's lawyers argued that he had been freed on $1 million bail and pleaded not guilty in the Los Angeles case but was jailed again after an arrest warrant was issued last week in Louisiana. They said an arrest warrant was not enough to hold Sharper without bail.
Prosecutors argued the paperwork is in order and that the athlete should remain behind bars until the extradition issue is resolved.
The judge set a hearing for next Thursday to give Louisiana prosecutors time to charge Sharper or for that state's governor to seek his return through another type of warrant.
Sharper, 38, has several ongoing sexual assault investigations in Louisiana, California, Florida, Arizona and Nevada.
In a bail motion filed last month, Los Angeles County Investigator John Maccharella described a pattern in which the former football star met women at clubs or parties and lured them to a hotel room, where they were allegedly drugged and raped.
The New Orleans warrant says police learned from witnesses that Sharper and associate Erik Nunez had acknowledged having nonconsensual sex with two women.
It does not elaborate on how the information was obtained or disclose the names of the witnesses.
"Through further investigation by the detective's it was learned that Nunez and Sharper admitted to other known witnesses that he and Sharper had vaginal and/or oral sex with victim's #1 and #2 without their knowledge or permission," the warrant states.
Sharper's attorneys say he never made such statements and the arrest warrant was a pretext to hold him indefinitely without bail.
Prosecutors, however, said they were following the law.
Chris Bowman, a spokesman for New Orleans District Attorney Leon A. Cannizzaro Jr., said he could not comment on whether Sharper would be charged before the Thursday deadline set by Judge Korn.
"It's an open investigation," Bowman said. "I'm not going to comment on it. I'm not going to put a timetable on it."
In Los Angeles, Deputy District Attorney Javan Wygal said it would be difficult for Louisiana authorities to prosecute Sharper because under the laws of that state, the case there would expire within four months if Sharper isn't tried.
Sharper was selected All-Pro six times and chosen for the Pro Bowl five times. He played in two Super Bowls, one with the Green Bay Packers as a rookie and was part of a successful championship run while with the New Orleans Saints.
He retired after the 2010 season and was working as an analyst for the NFL Network before being fired last week.
Leonard Levine, a lawyer for Sharper in Los Angeles, has said Sharper will be cleared in the cases.
"All of these were consensual contact between Mr. Sharper and women who wanted to be in his company," Levine said after a court hearing last month.
The Associated Press contributed to this report