Japaneses visa taking time

I got an Offer letter from a Japanese Prominent IT Company. They will manage Certificate of Eligibility as Skilled Labor for 5 years. I submitted the visa application form along with all related document 26/08/2018 , they collected all original copy and photocopy. They will not provide me any specific date for collecting passport . After 15 days gone I don't get any call from Local Embassy.
I talked with my senior normally I it takes 5 working days. I called them, they told us it might take 2-3 months to get visa if you have COE.
I am worried cause my joining date is coming soon, need time for mental preparation.
Can anyone explain me why it's take time ??

It takes as long as it takes. You are not the only person in the world that is applying for coe and/or visa.

Is their any possibility to reject visa, when you submit apply visa including COE ?

CoE does not grand you will receive Visa.

Visa will be given upon arrival.

But normally you do not need to be worried

"Visa will be given upon arrival."

Are you sure about that? Not everyone have this privilege, and it is usually for temporary/visitor visa only.
Furthermore this is for work visa, which you DO require to apply visa at Japan embassy with COE.

To OP/Guest, at some country visa application can takes longer time.
Is the senior you talked to come from the same country ?

Also something may have come up during your visa application, which may extend your application period.
Check with the embassy again.

"Is their any possibility to reject visa, when you submit apply visa including COE ?"
Yes, possibilities is there but no one can say for certain. Something like your visa application information do not match COE information. So many possibilities. But normally having COE does make the visa application easier to approve.

It is up to the embassy.

Thanks for reply,

My senior person in same country Bangladesh.

I got a phone call from the Japanese Embassy on the last day. They told me to collect my passport in next Sunday (16th September).
I asked her am I get visa on the passport ? She told me she cannot inform my visa status now.

"Visa will be given upon arrival."

Are you sure about that? Not everyone have this privilege, and it is usually for temporary/visitor visa only.

You are both wrong. Japan never grants visas on arrival. What you get on arrival is a landing permission, which usually, but not always, requires you to have previously obtained a visa at a Japanese consulate.