The rape complaint was filed on Saturday, March 27, but the 7-year-old girl was only called in to give a statement three days later, on Tuesday, March 30, according to the report.
While the US State Department has declared them a human rights violation, child marriages are currently still legal in at least 13 US states.
"She is four and a half years old," said the girl's father. "His punishment isn't even as long as her age."
The suspected parents have denied all accusations made against them.
The mother is the next in line to be investigated.
Hadiqa Bashir works in Swat Valley, until recently a Pakistani Taliban stronghold.