The Justice Department went to federal court yesterday to try to stop publication of former CIA agent Philip Agee's latest book, "Dirty Work II: The CIA in Africa," unaware that it has already been on sale in at least one Washington bookstore.

The government, in papers filed in U.S. District Court here, also seeks damages from Agee, a critic of U.S. intelligence policies. The government alleges that Agee, who now lives in West Germany, has repeatedly breached a secrecy agreement he signed while with the agency.

Agee's prior publications, "Dirty Work: The CIA in Western Europe" and numerous articles, which named alleged CIA undercover agents, were not submitted to the agency for prepublication review, a violation of the secrecy agreement, the government said yesterday.

The government's latest move against Agee came by way of a Freedom of Information Act claim filed against the CIA by Agee in November in federal court. In an unusual procedural maneuver, the government now wants to intervene in that case, contending that by his action, Agee has put himself in the jurisdiction of the U.S. courts for the first time since leaving this country 11 years ago.

In another development, the U.S. Court of Appeals agreed yesterday to delay returning Agee's passport, which was revoked by the State Department in December, until arguments on that decision are heard by the court.

Last month, U.S. District Court Judge Gerhard A. Gesell ordered the passport returned, ruling that Secretary of State Cyrus R. Vance had exceeded his authority. Vance had claimed Agee's activities abroad threatened national security and foreign policy.