The Colonial Ministry of Defense was the branch of the Colonial Government whose function was to research improvments in technology that can more effectively defend the Twelve Colonies from the Cylon threat if they ever decide to return.
Dr. Gaius Baltar was a consultant for the Ministry and worked on the development of the Command Navigation Program which became an integral part of much of the Colonial Defense Force's systems. Number Six did not work at the Ministry (Baltar implied that Six worked as a contractor that would get an advantage in future work for the Ministry in exchange for her help), but tagged along with Baltar as a guest while assisting him with creating the CNP, accessing the Colonial Defense Mainframe located in their main building.
Six not only fixed over half of Baltar's CNP programming algorithms for him, she secretly added backdoors into the program that would spell the doom of the Twelve Colonies as Baltar knew it (Mini-Series).
Dr. Amorak also worked at the Ministry. When a copy of Number Six appeared on Galactica under the alias of Shelly Godfrey, she pretended to be a systems analyst at the Ministry and the lover of Dr. Amorak (Six Degrees of Separation).
Amorak was aboard the Olympic Carrier and requested an audience with Laura Roslin with proof of a traitor in the Fleet. Before Amorak could give Roslin this information, the Carrier was abducted by the Cylons, who placed a nuclear weapon aboard the Intersun starliner and tried to destroy Galactica and her Fleet with the starliner before Vipers destroyed the ship, ostensibly killing Amorak as well (33).