Taking into account our legal system, it highly unlikely for a non-family member to be given custody of a young girl placed in a Nari-Niketan, as per a court order. You can approach the National Commission for Women (NCW) for their support in intervention in this matter. If you present a strong enough case on why this child should be allowed custody to you then they just might take the matter up with the authorities. The NCW has offices in every state.
Alternatively, an NGO can be approached for assistance in the matter. The NGO should be one of repute, with a history of helping women in distress. They will know the right offices to approach and procedures to follow.
Another thing that can be done is to counsel the father. Children make mistakes, they cannot be held guilty for their error of judgement for the rest of their lives. If the father did not want the daughter back, why did he file a police complaint? The man is perhaps bitter and angry, but there is nothing that cannot be resolved with some sound advice. Speak to him – his daughter is his flesh and blood. He might not be accepting her because of what society will say. Tell him he should make his own rules, not society. Why punish the child for an act that was perhaps done out of love/infatuation.
The parent had somehow failed the child, which is why she ran away. If the parent was open with the child, this would perhaps not have happened. The parent is further alienating himself from the child by shunning/abandoning her. In doing so he is committing to another failure and lapsing in his duty as a parent. Let him know that.