"Dozo, please take a seat," said the guy at the city hall. "Thank you," I said, not making a move. He rounded up some papers and came back to the table, "Dozo, please take a seat." But I just stood there, while he sat down.
For the man at the city hall, my behavior was nothing unusual. Japanese often don't make direct moves or respond after the first offer of something, apparently out of politeness.
Personally, I think it's more polite to do as you're told, but this is Japan. Hesitation exudes politeness.