The action has been taken based on report of a team sent to New Zealand last month by the Ministry to conduct an independent inquiry following the allegations.
The victim, believed to be a chef, had walked 20 kms one night from the diplomat's residence to Wellington where he was found by member of a public in a distress state.
External Affairs Ministry Spokesperson Vikas Swarup said the issue was first brought to the Ministry's notice on May 10 when one of the Service Staff Members of the High Commission was found missing.
"Though no charges were pressed by the Service Staff member, the Ministry will investigate the matter further. The High Commissioner has been posted back to Headquarters," he said.
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Swarup said the High Commission had immediately informed both New Zealand Police and Foreign Office and authorities reverted with the information that the staff member presented himself to the police on May 11 and made certain allegations.
"The team liaised with the New Zealand authorities to resolve the matter. The team also facilitated the return of the Service Staff member who wanted to return to India. He returned on May 28," Swarup said.
Meanwhile, New Zealand media said Thapar is set to leave the country today and a vehicle was seen this morning at his Wellington address.
Also, New Zealand's Ministry of Foreign Affairs and Trade said it is aware Thapar is preparing to leave the country.
"MFAT has been advised the individual concerned elected not to take the matter further. That staff member had independent legal representation and decided to return to India.