Colonial Intelligence began eons ago with the first planetary conflict on Caprica. As with most governmental agencies, it never seemed to disappear, but instead has grown steadily larger over the yahren.
Today, two main agencies work in the colonial government. CIS and the ICA. The CIS stands for Colonial Intelligence Service. It was started during the initial stages of colonial unification. The CIS was intended to help root out dissadents against unification and to help standardize all intelligence agencies into one. The CIS now mainly is used to spy on Cylon affairs. Not much information is available on the CIS concerning Cylon affairs. The agency is the most secretive department of government. It is known that they conduct spying and sabatoge missions frequently within Cylon borders.
The ICA stands for Inter-Colonial Agency. This intelligence agency mainly works with the colonial police force to keep crime down and reduce traitorous acts within the colonies. An interesting note is that Baltar started out as an ICA agent. He maintained a high profile with the agency and was able to bribe most of the agents and thus keep his deal with the Cylons secretive. This unfortunately lead to the holocaust and the near destruction of the colonies.