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.
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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.