“Please do not contact my current employer”

So I applied for a new job, and in the cover letter I had a line (to paraphrase) that said, “I have not included my current supervisor in my reference section for confidentiality reasons.” (For context I used past supervisors as references)

Well the new job called to set up an interview, and they sent over a pre-employment application, and it has a section for an employment record. Should I reiterate that they should not contact my current supervisor due to confidentiality reasons on the application? Or is the cover letter sufficient?

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