Hadnott took the girl to his home after offering her a ride on his motorbike. She began crying, and he offered to take her home in his car, where he allegedly raped her, according to police accounts.
Japanese police said Hadnott, 38, had admitted forcing down the teenager and kissing her, but denied raping her.
Hadnott's release came just two days after a visit to Japan by Condoleezza Rice, US secretary of state, who offered an apology to Japan.
Daisuke Ebihara, the head of a group of victims of crimes linked to US soldiers in Okinawa, alleged that the girl's family had been put under pressure.
Ebihara said: "It's extremely regrettable to hear this news just at a time when we were building up a movement on the case. "
He said: "I understand that this case was sensitive, especially for the victim. I wonder if there may have been any pressure on her to drop the case."
Masahiko Komura, the Japanese foreign minister, had warned that the case would stir up an opposition to US bases.
The case has been the most high profile of a series of incidents on Okinawa.
Authorities are also investigating allegations that a US serviceman raped a Filipina in a hotel on February 18.
Three US troops gang-raped a 12-year-old girl in 1995, setting off major protests that set in motion a process to withdraw thousands of troops from Okinawa.