The idea for a Minecraft Lego set was submitted by Mojang (Minecraft's publisher) to CUUSSO, Lego's crowd sourced submission site. In CUUSSO a user submits the idea for a set and the public votes on them. Any sets that receive 10,000 votes is submitted to a Lego Jury who determine wether or not a project is feasible. The Minecarft concept broke Lego CUUSSO records, reaching the 10,000 vote mark in less than 48 hours. Today the Lego CUUSO blog published the news that Minecraft fans had been waiting to hear:
We're happy to announce that the Minecraft project on LEGO CUUSOO has passed the LEGO review and we are now developing a concept that celebrates the best aspects of building with the LEGO system and in Minecraft. We can’t wait to show it to you—but it isn't ready just yet. These things take time, so we appreciate your patience. More details are to come.
Since this was the official Mojang endorsed effort, they will be able to work with Lego to secure licensing. As the "owner" of the project Mojang will receive 1% of sales, which they have pledged to donate to charity. I'm assuming they will also receive licensing fees, but due to the weird nature of the collaboration it's hard to say.