I've been hired but I live overseas...

Hello, everybody. Here is my situation: in March, soon after Japan banned foreigner travelers and residents being abroad from entering the country, I was hired by a Japanese company. Fastforward to June and I've sent all the needed documents in order to obtain the COE, which is of course mandatory to get a working visa. The company did tell me that the issuing of the COE will take some time so I have to wait. Now here's my question: is it sure that the immigration bureau will issue the COE with everything that is going on with the coronavirus? If so, how much do I have to wait? I think that the company sent my application in mid-June so I don't think they will contact me any time soon, but what if two, three months pass and there is still no progress? Should I contact the company and ask them about the situation?
I would like to hear your opinions and maybe confront the situation with people with similar circumstances. Thank you (and sorry for my English, it's not my first language)!

During this time, the process has been slowed down for processing visas and COEs. Personally, I would just wait a little longer as it depends on a case by case basis.

If it's been over a month, you can inquire at the company and ask if they've heard an update. Usually the company will inform you when you get information from immigration about those kinds of things.

General guidance for CoE in normal times is three months.
However, until travel restrictions are lifted/eased you wouldn't be able to get into the country.
Coming for a job might fit into their "business" travel definition, but that will be some stage after they let other legal residents back in.