Wesley Mathews, 37, was arrested after the Indian- American changed his story about his adoptive daughter Sherin's mysterious disappearance over two weeks ago, police in Richardson city, Texas, said.
Mathews had previously claimed that Sherin went missing after he sent her outside their home at around 3 a.m. on October 7 as punishment for not drinking her milk.
The particulars of his statements that might have led to the charge have not yet been explained by authorities.
Mathews, who hails from Kerala, was booked into the Richardson City Jail on a USD one million bond.
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First-degree felony injury to a child is punishable by up to life imprisonment or from five to 99 years in prison, US media reported.
Mathews and his wife Sini reportedly adopted Sherin two years ago from an orphanage in Bihar.
Yesterday, the Richardson Police announced that they discovered the remains of a small child in a tunnel beneath a road, expressing apprehension that it was "most likely" that of Sherin. They, however, did not confirm the identity.
The body was discovered in a culvert beneath a road with the help of search dogs. Police have not released any details about how the child died. The body was found about one km from the house of Mathews.
The father was previously arrested and charged with felony endangerment to a child and was placed on electronic ankle monitoring. He surrendered his passport as a condition of making bond on October 9. He was later released.
Child Protective Services took custody of the Indian- American couple's other biological daughter shortly after Mathews was arrested.
Sini Mathews, the girl's mother does not face any charges. She was in the house at the time, but was reportedly asleep and unaware of what her husband was doing, police had said earlier.
But the judge at a Dallas County court decided that the older sibling of Sherin will remain in foster care for at least three more weeks.
The judge postponed custody hearing until November 13 to allow Mathews to hire a civil attorney.
The girl will remain in foster care until that hearing or until a judge orders a change in custody, said Marissa Gonzales, a spokeswoman for Child Protective Services.
"We can begin looking into those relatives, but it is entirely up to the judge where she is placed," she said.
On Monday evening, people gathered near the culvert where police found the body of a small child.
Many people expressed shock at the father's second arrest.
"Justice should be done for this little child," said Indian-American Anthony Sabu. "This little child has gone through the worst things in her life. She was abandoned when she was born and this family adopted her, and this is not what we expected," Sabu was quoted as saying by NBC News.
"We are deeply concerned about the missing child. Indian Embassy in US is actively involved and they keep me informed," Swaraj tweeted on October 19.
"We are closely monitoring the Sherin Mathews case. We have established contact with the community and authorities," India's Consul General in Houston, Anupam Ray had tweeted.