It depends on context, I would say. Opere citato would mean "from the cited work" or "in the cited work" in the most relevant contexts. Opus citatum would mean "the cited work", where it could be subject or object or possibly something else. Operis citati would mean "of the cited work".
If it is a Latin text, the phrase would be expected to follow ordinary Latin rules of inflexion. If you see it in e.g. an English text, it would depend on the sentence; can you replace it with "in the cited work" or "from the cited work"? Then it should stand for opere citato. Would you rather replace it with "the cited work" without a preposition, when you're making it fit in the English sentence? Then it should stand for opus citatum. This is also the base form of the word (the nominative). And "of the cited work" corresponds to operis citati.
But it's ultimately not extremely important: as long as it's abbreviated, they all look the same. And it's not often easy to tell which form would fit best.
In a footnote: Aristotle, op. cit. [opus citatum, as the base form probably fits best, but I'd say opere citato could work as well]
This is similar to a passage from chapter VII op. cit. [here operis citati would probably fit best, but a case can be made for opere citato]
The theory is mentioned in op. cit. as well [since we can't have "in in", nor "in of", a plain opus citatum would make the most sense; but I suspect some people might object to this usage altogether, with the English praeposition]
Examples can be found everywhere op. cit. [opere citato would fit best here, but this is perhaps a bit contrived]