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I have finished my Masters in physics in 2020. After two years of work experience as a research associate, I secured PhD at a good university. My adviser took me solely because of my old advisor's recommendation and now is unhappy for two reasons:

  1. the old advisor is not collaborating with my new advisor because of the personal disputes between me and my old supervisor
  2. He thinks that I am not fit for the program.

The government doesn't allow to fire PhDs so he said he would want to step down as an advisor as he thinks I am not qualified for research. I have been having issues with meeting deadlines and it feels like an anxious battle every time I meet him, that is, if I do not cancel the meeting. My PhD coordinator has already advised me to cooperate with my advisor and now my supervisor has reached out to our coordinator again to step down as an advisor.

I was enthusiastic and now I even think I might not be good enough for PhD. I am even planning to consider another masters. I am at crossroads, I want to complete my PhD but I feel ashamed to even go to the department. What should I do?

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We don't usually do personal advice on this site, but since your kind of questions are so common I will take a stab.

Most importantly:

You are still early in your PhD, so get out. Change supervisors in the same university if possible, or change universities if not. It sounds like you are about a year into the program and you already have serious anxiety about meeting your advisor, and your advisor has formally asked to step down from advising you. This isn't working, and it's not going to get better. I feel confident in saying that you aren't going to graduate in this exact setting, and even if you do it will take so much of a hit on your mental health that it won't be worth it.

I was enthusiastic and now I even think I might not be good enough for PhD. I am even planning to consider another masters.

From what you write, your relationship with your PhD advisor was kind of toxic from the start. Failing in such a situation does not mean that one is not cut out for a PhD.

The good news is that you now know a lot more about what you are looking for in a supervisor, and what you don't want in a supervisor. If possible (and based on the response from the program coordinator it sounds like this would be possible), find a new supervisor in the same program that better suits you, and remember the common adage that "supervisor fit" is more important than "research topic fit" - it's easier to learn to love a research topic that wasn't on the forefront of your mind before starting than to work for years with a person you don't gel with. I would argue that this is particularly true in your case, where there is by now a certain level of emotional baggage that a new supervisor would need to handle.

I know that it's difficult to "write off" a year or longer, but in the grand scheme of your career (or even your PhD studies) a year really isn't that much. And, if you browse the archive of questions on this site, you will see that working with a supervisor who does not want to advise you is substantially worse than writing off a year of studies as a learning experience.

Good luck!

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