The Bureau of Immigration has been asked to explain the circumstances leading to the deportation of former diplomat Kurt Vogele, a home ministry official said.
Vogele, who had served in India, was deported soon after he landed in Ahmedabad on January 22.
He was allegedly told he had "no right" to enter India and was "deported" without explanation. His passport was returned in Geneva.
In a letter to Sibi George, Indian Ambassador to Switzerland, Vogele demanded to know the reason for the "blacklisting".
Reports said SDC was understood to have funded a Dalit rights organisation-Navsarjan Trust- whose Foreign Contribution Regulation Act (FCRA) licence was cancelled in 2016 over allegations of engaging in "undesirable activities" that could disturb harmony.