I spent 5 years on my mechanical engineering PhD. I think that my thesis work could have been done in 2 years by a serious student. I have wasted my time on futile work.
I don't know how to justify the length of time spent working on my PhD and my low research output to my committee.
With hindsight most PhD theses could have been done a lot quicker, but we typically don't start with hindsight. Moreover, you are supposed to learn while doing your PhD thesis. So again, someone with the experience learned from doing a PhD might have avoided some of the futile work (but see my first point), but that is not a fair comparison. So the first thing you need to ask yourself is: are you fair towards yourself.
There is a LOT of dead time during a PhD. I've had friends spend years on projects that never came to anything. Some people are luckier than others - and any examiner will know this.
The main reason not to worry is that they shouldn't ever take into account the time taken to produce the thesis, only the quality of the thesis itself. They don't hold you to a higher standard if you took five years to complete than if you took three. A thesis is a thesis! Don't panic, and you'll be absolutely fine!
Worry not. You dont need to justify your time, you only need to justify your thesis and what is written in it. Anything else wont exist for the duration of the defense exam. You are there to defend the data and results of your research, and any question outside of that you can redirect back to your thesis.
For example, if you have a research in pokemon evolution and you are asked about the time of the research, you says that the methods presented on your thesis, in Chapter 2, section 'XXXXXX' denote the process's own time, and therefore help validate the results, which are appropriately and consciously revised as can be seen in the conclusions chapter in section 'YYYYYY', which point to the prof/disproof of the original hypothesis.
Remember that you are defending your thesis, it's methods, and the results (and maybe, awfully too, the historical/theoretical frames). Unrelated questions are actually tricks from the examiners to derail you.
Even without knowing any further details, it is clear that you are too hard on yorself. Doing a PhD is not about doing a certain amount of work and then graduating.
You need to learn new skills, research and keep adapting until you find out in which direction to go and how your contribution is going to be. So in those 5 years you did much more than just the contribution itself.
You are not alone in thinking this way, as someone mentioned, check "imposter syndrome".
This is an old question, but perhaps some people are in the same position, so...
I've just come through my viva - in computer science in the UK. I had a lot of the same anxieties, but I did know that in the viva they were checking:
whether it was clear that I understood what I had done and why I had done it
whether I could justify my work's novelty - not that it was somehow ground-breaking, but that it explored a specific avenue that hadn't already been investigated and reported
whether my thesis made sense, i.e. were the experiments relevant, fair, well reported and analysed, and was the story told reasonably well from motivation through to related work, analysis, and conclusion
was it a significant contribution to the field
I guess it's that last one that was bothering the poster. The examiners didn't care about the time spent, just whether the work was substantial enough to make it more than "just" a Masters level piece of work. That judgement could be on the scope of the work, on the novelty, on the thoroughness of the analysis, but never on the number of hours spent on it - they didn't ask and I don't think they care.
As others have said, the PhD programme is in a way distinct from the PhD thesis. In those 3+ years you're supposed to be apprenticed into academia, learning skills, developing networks, trying your hand in submitting and reviewing work at various levels, etc. This programme is tested indirectly in the thesis and the oral defence in the sense that if the journey has been successful then your work is of a certain quality (not exceptional, world-beating, just good enough to be of interest to the relevant research community).
In either case, once it's submitted there not much you can do about the thesis, but in preparation for the viva you can ensure you've re-read your work thoroughly (warning, you may spot mistakes afresh) and that you can justify your decisions and omissions. There are useful lists out there with common viva questions, but they can be quite overwhelming especially if you don't have loads of time to prepare.
I was given the opportunity to kick off the viva with a 10 minute presentation setting out the motivation and chief contributions - this was a nice way to remind myself and the examiners of the big picture. This might be a good preparation activity even if you don't actually present it on the day.
