During the defense, how to prove the method I used in my master thesis is correct? I will have my master thesis defense in one week and today my advisor wrote me he is not sure about a method I used to obtain a result (this will not ruin the entire work, but still will make some results useless). 

I explained him the theory behind the method (which I found in a highly reccomended book, and I decided to apply after having written to the book's author to ask clarifications), but still he keeps raising doubts about it.

The fact is that now it is too late to change things, because the thesis has already been registered and anyway I do not understand why the method should be wrong. Therefore I stick to what is written in the book and to the explanation the author gave me. 

I thought that maybe he just want to make sure I will be prepared to defend my work that day, but he is actually having words on the method itself, which is not something I have invented: I am just applying it as it was explained.

This is making me really anxious, because I do not know how to deal with this if such a question should be asked during the defense. I mean, I will give the same explanation, but what if someone insist on it?
This is not something you should get to your defense with your advisor still doubting. You and he need to sit down ASAP, work through the material, and not stop until he is satisfied. I would would hope that he would be willing to take this very seriously. No advisor should let a thesis go to a public defense with this kind of question looming in their mind. No one should be forced to do a defense that their advisor thinks they're not ready for.