Social Justice and Empowerment Minister Thawaar Chand Gehlot saw off Geeta at the airport who was accompanied by officials from the Indore-based institution.
"Geeta has gone back to Indore," External Affairs Ministry Spokesperson Vikas Swarup said.
Earlier in the day met President Pranab Mukherjee and Delhi Chief Minister Arvind Kejriwal.
Geeta, who had accidentally crossed over to Pakistan over a decade ago, had returned here to a grand welcome yesterday. However, she had failed to recognise a family which she had initially identified from photographs.
Swaraj said Geeta will be kept in the Indore institution for hearing-impaired people till her "real family" was found.
Swaraj had said Geeta's DNA sample was being examined and if it does not match with the samples of the Mahato couple, then government will start afresh the process to find her parents.
"If the DNA samples match, then it will be a complex situation. We will ask Geeta to recollect things and go down the memory lane. We will make her sit again with them (Mahatos) so that she recollects her memory," the minister had said.
She was adopted by the Edhi Foundation's Bilquis Edhi and lived with her in Karachi. Bilquis and her grandchildren, Saba and Saad Edhi, accompanied Geeta here.
Her story came to light after the release of Salman Khan starrer 'Bajrangi Bhaijaan' in which the hero unites a girl separated from her Pakistani mother who was visiting India.
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