When writing four part counterpoint in context of the common practice period it is common to omit the 5th of a chord when in a jam. Is it always ok to omit the 5th and are there times when the 5th of a chord are required?
In counterpoint, "chords" are incidental - the result of proper voice-leading rules and carefully controlled dissonance. What matters more is whether or not all of the intervals are consonant, and if they are not, how you are controlling the dissonance (whether or not it is being handled appropriately.)
Because the rules are the way they are, then lend themselves quite naturally to creating nice root position triads (after all, what is a triad if not two consonances?)
Chances are if you are in a really bad situation, that means that there is an error occurring previously in your line(s). I would go back, re-work your lines and see if that clears up your issue.
David Cope in "Computer Models of Musical Creativity" points out (rare) cases where Bach used parallel fifths in his chorales. In analysis, the alternatives are less satisfactory than Bach's use of the parallel fifth. Students of counterpoint, however, will very likely be expected to find some other way to resolve such a case that does not involve simply omitting the 5th (as then you're either doubling the 3rd, which may be frowned on, or doubling at an octave, also could be bad, or oops dissonant 7th now that needs proper handling or maybe try to slide by with oblique motion but the teacher is frowning and reaching for the red pen...).