I am not a native speaker but I am not sure if putting "fluent" in the
form will make it look like I have some deficiencies in the language.
Which one should I choose?
If you aren't a native speaker (and you indicated that you are not), then you shouldn't claim to be, because that is called lying.
That's why they have two distinct choices - to separate those who have this as a first language and who have learned to speak the language fluently later in life.
Few companies want to hire an extremely fluent liar.
In this case, you must either choose "Fluent", or leave the question blank, and hope they don't really care.
You are free to expound on your language capabilities in your cover letter. And of course your interview gives you the chance to demonstrate your language abilities in all the languages in which you are fluent.
And you are free to avoid answering any questions you would rather not answer, at the risk of being rejected for not following directions.
If you conclude (as some apparently do), that the question itself is evidence of discrimination, then you might choose to sue the company, or might decide to just bow out of the application process completely, since you wouldn't want to be involved in a discriminatory workplace.
[Note: I'm not saying the question makes any sense. I'm not saying I'd ever ask the question. I know companies that do ask this question. And I know what I (and most hiring managers) think of applicants who give false answers to whatever question their company chooses to pose.]