The ink should not be applied to left-hand fingers of a person so as to avoid confusion during voting, it said.
Election Commission of India (ECI) has also written to the Union government on the same issue.
"SECM has said the ink mark should not be applied to the fingers of the left hand (at banks while swapping demonetised notes)," an official of the poll regulatory authority said.
Elections to 192 municipal councils and 20 nagar panchayats will be held in four stages -- on November 27, December 14 and 18 and January 8.