To say that someone is "not in his seat" suggests that the person is required, or at least expected, to be seated. For example, a teacher may get annoyed if a child is not in his seat at school. It's not likely you need to tell someone on the phone that someone is not sitting down when he is supposed to be.
In contrast, in American business, you could say "He's not at his desk right now." He may be in a meeting, home sick that day, getting a cup of coffee, or picking up something from the printer. You don't know where he is, but you can see that he's not at his desk/work station. Where I've worked, it's common to leave your phone message as "I'm not at my desk right now, so please leave a message and..."
However, a generic thing to say is "He's not here at the moment."
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