"We are thankful to Indian authorities for their cooperation in this humanitarian matter," Pakistan's High Commissioner to India Abdul Basit tweeted.
The boy, Iftikhar Ahmed, was yesterday handed over to Pakistan Rangers by Indian authorities at Wagah where his mother was waiting for him for several hours.
"I am extremely happy to have my son back. I am thankful to the Pakistani government for its help for return of my child," Iftikhar's mother Rohina Kiyani had said yesterday at Wagah.
The boy's mother alleged that her estranged husband, who hails from Jammu and Kashmir, had lied to her that he was taking the child to a wedding along with him as he took him to Dubai and from there to Kashmir in March 2016.
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Rohina with the help of Pakistan High Commission in New Delhi had filed a custody case in an Indian court.
After the case was taken up by the Pakistani High Commission and proven that Iftikhar was a Pakistani by nationality, the court ruled in her favour and ordered that the child should be returned to his mother in Pakistan.