Dr Cecil Joseph, a Stephen's alumnus who is currently an adjunct faculty member at the University of Massachusetts Lowell, had applied for the post of Assistant professor in the physics department and was selected for the same.
However, after the hiring sparked allegations that the college's selection process was skewed in favour of Christians, Joseph turned down the position.
An alumni group, which is not officially recognised by the college, has claimed that a 'conflict of interest' was the reason behind him refusing the post as Joseph is the son of a member of the college's Supreme Council and Governing Body.
He said that Joseph was "the most competent candidate among those who had applied for the job and he genuinely wanted to serve his alma mater".
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"I have humbly requested him (Joseph) to reconsider his decision, but he has not responded yet," Thampu added.
Thampu also rapped the alumni group, saying, "A selective group is making an attempt to give a communal flavour to a fair and transparent appointment process. These attacks are hampering the reputation of a college which is a national treasure."
"Joseph... Wanted to serve his alma mater despite having a full-time and lucrative position in a US university.
"If he doesn't reconsider his decision we will lose out on a quality teacher and, if such campaigns continue, the college will continue to suffer," he added.