John Cridland said the application to register "should not have been made", as it had not been approved by the CBI board and was not signed by an authorised signatory.
He added that the business lobby organisation had now contacted the Electoral Commission in a bid to "deregister our position".
The move comes just over a week after it was revealed the body had registered with the Commission to formally back a No vote in the Scottish independence referendum.
At the time a CBI spokesman said it had done so "in accordance with the law".
But the move sparked a backlash that saw 18 bodies - including several Scottish universities, the BBC and broadcaster STV - either resign or suspend their membership of the CBI.
Mr Cridland said registering with the Electoral Commission had "triggered something none of us expected".
The CBI - whose members include 1200 business that operate in Scotland - has now conducted a review and taken legal advice from a QC.