Mojang is in the process of supporting mod development for Minecraft.
According to Mojang, via RPS, the plan is to build a "fresh server API" and then extend it to support client-side modding using Bukkit as the server mod.
Mojang said it will provide the same flexibility as with the official Minecraft server.
“The plan is to build a fresh server API, and then extend it to support client-side modding (in one way or another), 'said the firm. "We will try to make it easy for Bukkit users to convert if they wish to do so, but backwards compatibility is not guaranteed.
"We will, however, help Bukkit to be compatible with 1.2, to avoid having a long gap while you wait for the official Minecraft server to catch up. We hope that this will help the quality of Minecraft multi-player to improve, both for large and private family servers, while still being able to add fun stuff for the bigger audience.”
This means the current API will be ditched for a new one so mod support can be better handled.
An ETA wasn't provided.