The girl's body was recovered from the Rassana forest on January 17, a week after she went missing while grazing horses.
The issue had repeatedly rocked the state Assembly with opposition parties raising questions and demanding action against the culprits.
On January 23, the Mehbooba Mufti government had ordered a probe in the kidnapping and killing of the girl and handed over the case to the crime branch of the state police.
"We are taking services of the forensic science department to investigate the alleged rape," he said.
With the arrest of the SPO, the number of arrests in the case has gone up to two.
A special investigation team (SIT), constituted by the state police, had arrested a 15-year-old boy and claimed the accused had strangulated the victim after she resisted his rape attempt.
The government ordered suspension of an station house officer on January 20.
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