I think Pelin ask more questions than anyone on the site. :) Always something new and I like that.
Anyway, the answer is yes.
Teacher to Student - "I want to have a word with you." Students inner thought might be "oh no, what have I done now"?
Boss to employee. - "I want a word with you" - Same as above. "Oh no, have I done something wrong?
The tone of the voice when the person says this can also have bearing.
Ways to say this without making someone have fear about what they talk may be about:
1. I would like to have a word with you.
2. I would like to speak with you.
3. When you get a few minutes I'd like to sit down and talk.
4. I would like to go over a few things with you.
I hope this helps,