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.
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I may be wrong on this because I think this is to be left up to opinion, but my theory teacher said that you can omit the fifth in a traditional setting only for extended chords like a seventh or a fully diminished, and not to omit the fifth in any form of triad.