For such situations, our elders have Dhyana Shloka which is recited before commencing the japam. Try and understand the meaning of the Dhyana Shloka. This Shloka contains the description of the form of the deity upon which the japam is done and methods to meditate upon that deity.
While performing japam, external thoughts afflict one when one does not meditate upon the divine form of Bhagavan. To the extent possible, learn to meditate upon a form of Perumal and this will prevent external thoughts from coming in during japam.