This is caused by either Tuberculosis or an Aeromonas bacterial infection. The tuberculosis is not, unfortunately treatable, and will not respond to treatments or anti-biotic injections and furthermore this form of Tuberculosis is even potentially transmissible to people and extreme care should be taken if you are sure that what your koi has is tuberculosis.

If; however, it's an Aeromonas infection, it may respond to injections of antibiotics and topical dressings such as Koi Doc wound dressing, but sadly the hole will not close. Check for, or treat for a concurrent parasitism and for best results, ensure optimal water quality, temperature and aeration.