Justice V Ramasubramanian stayed the November 21 order of the ministry and issued notices returnable in three weeks.
Natarajan was nominated to the post of vice-chairperson by the previous UPA government on February 25, 2014 for a period of three years.
Noting that he was associated with CICT since its inception, the judge said he fulfilled all norms required for the post. On November 21, he received a scanned copy of his termination orders issued by the HRD ministry without assigning any reason.
Contrary to rules, Natarajan was removed and a retired professor of Pachaiyappa's college P Prakasam was appointed in his place, the petition said.
The CICT, which is an autonomous body under the HRD ministry, has chief minister of Tamil Nadu as ex-officio Chairperson.