In order to prevent the body from rejecting an implanted magnet, it must be coated with a biocompatible material. In the past, others used implant-grade silicone. The magnet was dipped or the material was applied via a mold, completely encasing the magnet. (see Magnetic Implant: Development and Updates.)
Unfortunately, both the strength of silicone and the method used to apply it resulted in almost all of the implants failing. Silicone proved simply too soft to guarantee containment. In Shannon Laratt's final article about the implants he suggests immediate removal of any silicone coated magnets, as he their eventual failure is inevitable.
Encasing the magnet in Teflon or glass would be an option, but both those methods are currently beyond my means. Titanium or other implant grade metals could also be a possibility. Some of these methods require intense heat, which can demagnetize and damage a magnet.
The most attractive option (to me at least) is a Parylene coating. Parylene is a polymer which is applied in vapor form at room temperatures in a vacuum. Parylene is biocompatible and has been used for years to coat medical devices for implantation.
Right now the plan is to get magnets coated, test them out, and eventually have one implanted.