The accused, Purkha Ram, is on the run. Villagers found the bodies of the two children on Tuesday morning and informed the police.Pali superintendent of police Jai Narayan said the post-mortem was conducted at a private hospital. He added both the children were strangled.
"The accused fled the village after killing both his children. A case of rape and murder has been registered and police teams have been dispatched to nab him," said Narayan.
"The post-mortem report has confirmed that the girl was raped and strangled. Initial reports suggest strangulation was the cause behind both the deaths."
According to police, Ram married twice, but his wives parted ways with him. The children were from his second wife, who left him around three-four years back.
Narayan said Ram brought the children last week to his village from their grandmother's place.
Sex crimes and child abuse continue unabated in the country despite the government tightening anti-rape laws last year in the aftermath of the 16/12 incident.
Records show a rape is committed every 22 minutes in India, a nation of 1.2 billion people.
Addressing Parliament recently, Prime Minister Narendra Modi had touched upon the issue of women's safety against the backdrop of a spate of sex crimes.