The decision was taken at the general body meeting of the council, which accepted the recommendations of the executive committee for his removal, said a council statement issued by its chief executive and secretary Garry Arathoon.
Both the meetings were held back to back here.
CISCE conducts the ICSE board examinations across the country for all its affiliated schools.
Aikara could not be reached out for his reaction. He has been charged with "acts of omission and commission including acts of financial irregularities and violation of memorandum of association and rules and regulations of the council", the CISCE said.
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Immanuel is the principal of S D A Higher Secondary School.
Incidentally, the development comes close on the heels of the council revoking the suspension of Arathoon last month and reinstating him as the chief executive and secretary.
He was suspended by Aikara earlier this year for allegedly promoting textbooks written by wife without the council's consent.
The suspension was revoked after he apologised, sources said.