This question has been answered before, here and here by u/Profrock451 and u/SaneBRZ respectively.

In short, ambassadors were treated with respect and were held as prisoners of war until they could be exchanged with the enemy countries' ambassadors. This made sense, since harming the enemy countries' ambassadors would most definitely mean retaliation against your own countries' ambassadors.

Sugihara was a Japanese diplomat in Lithuania before the German invasion. Shortly before leaving to return to Japan after war broke out he spent days signing some 6,000 travel documents so that Jewish people could escape to safety. He reportedly spent 20 hours a day working on the visas and was said to have been working on them literally until he got on the train to leave, at which point he threw his official document and stamp out the window so people could make their own. He did all this despite knowing he could be killed for defying the Japanese government and spent the rest of his life in poverty after he was demoted.