The war of words came a day after US intelligence chiefs said North Korea probably had missiles capable of attacking America's west coast as well as one or two nuclear missiles.
Mr Ishiba said:
"Our nation will use military force as a self-defence measure if North Korea starts to resort to arms against Japan."
It was unclear exactly how Japan could respond to any threat. Its post-war constitution bans war as a means to settle international disputes and it also lacks the missile capability to be able to defend a nuclear strike.
Mr Ishiba proposed working with the U.S. in developing a joint defence system.
Japan is currently in talks with Washington over a "theatre missile defence system", a variant of the "Son of Star Wars" programme, aimed at shielding US troops in Asia.
Tokyo began examining the system after North Korea launched a ballistic missile that passed over Japan in 1998.
Tensions are running high over North Korea's suspected nuclear weapons programme.