The circular had directed local bodies to register marriages of Muslim women above 16 years and men who have not attained the age of 21 years.
Official sources said a fresh circular would be issued instructing civic authorities to ensure that the earlier circular would not be used as a pretext for child marriages.
The department has justified the circular on the ground that it was meant to overcome difficulties posed to Muslim couples who had already married in getting passports and other documents for migration to foreign countries for work.
Coming out strongly against the circular, Opposition leader and CPI-M veteran V S Achuthanandan said it went totally against the spirit of Constitution and a challenge to the law that fixed age of marriages for women at 18 and men at 21.
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Demanding its withdrawal in toto, CPI-M state secretary Pinarayi Vijayan termed it as a "dangerous" move and said progressive sections within the Muslim community itself had come out against it.
Pro-Left women and cultural organisations have come out against the circular, which, they said, would push the state to the medieval ages.
Kerala Institute of Local Administration Director P P Balan has also sought a clarification from the government on registering such marriages under the provisions of Kerala Registration of Marriages (Common) Rules.
Government's clarification is that Muslim Marriage Rules, 1957, did not insist on age limit and the Child Marriage Prevention Act, 2006 did not specify that marriage between men below 21 and women below 18 years was invalid. So marriages of Muslims not attaining the mandatory age could be registered.