Urgent! COE related question

Hi guys,

My boss recently set up an office in Japan and he wants to apply for a long-term stay visa and in order to get the visa you need a COE (yes, I'm his assistant that needs to figure out how to apply for visa). There's not much information online and everything is telling me that in order to get COE, he needs to submit the application in-person at the Immigration Office in Japan, which means I can't submit the application at a foreign embassy or mail the application). In this case, what should I do? Is there an alternative way to get a long-term work visa without the COE? Please please please someone help