Though the incident occurred on June 14, it came to light today after the girl's family lodged a police complaint.
The accused has been identified as K Ganesh (29), a native of Chodavaram and resident of Gajuwaka area of the city, said police.
Inspector of New Port Police station K Nageswara Rao said the victim is a Class V student and a resident of HB Colony area in the city.
Ganesh used to ply auto in the vicinity of the area and was aware of the girl's daily activities.
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He later dropped her home, said police.
The girl narrated the incident to her parents that night itself.
Police have registered a case under section 376 (rape) of IPC and under relevant sections of POCSO.
They have launched a manhunt to nab the accused who is absconding.