I've heard the Latin phrase imperio in imperium used in political discussions a few times. While I understand what the phrase literally means in Latin ("by command into command"), I'm not sure what the intended meaning is when the phrase is invoked in English as a discussion of political strategy or reality.
You are right that it would mean something like "in an empire into an empire", which is nonsense; fortunately, this phrase is wrong: the classic term is imperium in imperio, which is, as Alex explained, an "empire within an empire", a group or organisation that functions almost as its own state, even though it is officially not a state but merely an unofficial entity within a state. The use of the word "imperium" instead of a more neutral word meaning a commonwealth, like "res publica", implies that the leader(s) of this entity impose some rules on it that would normally be imposed by a formal government.
Further down on the page that Robusto linked to, the expression is defined: it means "a state within a state" - in other words, a group that exists within a political unit but exercises independent power there.
Examples they give include: the Catholic Church in England before the Act of Supremacy (which made the British monarch the head of the Church of England - i.e., it became subordinate and no longer a separate imperium), and the Mormons in early territorial Utah. Possibly another example might be the Inquisition in Spain, which was nominally under royal control but in practice operated pretty independently.
In politics, it refers to a sphere of power or dominion.