Method and system of increasing safety of ablation of cardiac arrythmias, especially AVNRT and antero-septal accessory pathway ablations. A computer based system acquires, conditions, and analyzes the timing relationships between atrial and ventricualr signals during normal sinus (NSR) and junctional rhythms (JR) during ablation. If the timing analyses determines a safety issue, such as loss of retrograde conduction during junction rhythm, while slow pathway modification is being performed, the computer electronically disconnects the ablation circuit. This immediately stops the energy delivery to the tissues and provides a chance to reposition the ablation catheter tip to a more safer location. The ablation may be using radiofrequency (RF), cryoablation, or with high intensity focused ultrasound (HIFU). The functionality and circuitry of the system may also be incorporated within an ablation generator, EP recording and monitoring system, or a cardiac mapping system.