The arrestee was identified as Mizan Sardar, a truck driver, of the area.
Quoting locals, Humayun Kabir, officer-in-charge of Khalispur Police Station, said Mizan started raping his girl when she was reading in Class-VI.
At one stage, the girl became pregnant and the father made her have an abortion at a private clinic, he said.
On Wednesday, Mizan attempted to rape the girl again around 10am at their house in Housing Old Colony when she raised alarm.
Hearing her screams, locals rushed in and rescued the girl and informed police.
On information, police arrested the accused father while the girl was taken to Khulna Medical College Hospital for medical test, the OC added.
In Khagrachhari, police on Tuesday night arrested a young man as he allegedly raped a six-year-old girl in Mahalchhari upazila in the district.
The arrestee was identified as Khorshed Alam, 22, son of Abdul Kuddus of Natunpara in the upazila.
Officer-in-charge of Mahalchhari Police Station Nure Alam Fakir said Khorshed violated the girl after taking her behind the Mahalchhari Hospital on Tuesday.
Later, the victim was admitted to Khagrachhari Sadar Hospital in a severe condition.
In Chandpur, police arrested a teacher of a private school early Wednesday in Hajiganj upazila as he had reportedly been violating a girl her for the past two years promising to marry.
The teacher was identified as Kawsar Hossain, 28, son of Md Shah Jamal of Noadda village in the upazila.
Officer-in-charge of Hajiganj Police Station Alamgir Hossain Roni said Kawsar had been in love with the victim for the past two years and he had developed physical relations with her promising to marry her.
But recently Kawsar refused to marry her which prompted the victim to file a case under the Women and Children Repression Prevention Act on Tuesday.
The accused was sent to jail after he was produced before a court on Wednesday, said the OC.