Berlin prosecutors were responsible because the main Stasi office was in East Berlin.
Berlin prosecutors are reportedly also preparing cases against dozens of other former East German officials.
But a new report issued by Berlin prosecutors says there were at least 350 victims, and perhaps as many as 400.
They are charged by the Berlin prosecutor with having imposed or accepted rules under which would-be refugees fleeing westward were shot dead by border guards.
"The law is simply not written for crimes like these," said Uta Folster, a spokeswoman for Berlin prosecutors.
For this reason alone, the petition to the Berlin prosecutor by a theology professor to reopen the case will in all probability not be granted.
One senior Berlin prosecutor, Dieter Neumann, denounced the decision as "patently absurd."
It is not clear whether Mr. Honecker will have any further contact with Berlin prosecutors.
Berlin prosecutors said the managers' homes had beenwere searched for evidence.
A spokesman for Berlin prosecutors said today that prosecutors are considering about 1,350 complaints against guards alleged to have shot at fleeing refugees.