Japanese Education
 

Does a 2 year secretarial course count as university in Japan?

lol (no)

Try a degree.

You will need to have a 4 year degree from an accredited university to count toward any visa, at the very least.

However, if you somehow magically manage to get a visa through another route - it will count as some level of education. (専門学校)

No. University in Japan is always four years. It may count as junior college or technical school, but it's not a degree I've ever heard of being offered in either of those. More likely, it would be considered as senshu gakko or kakushu gakko, which typically aren't accepted as formal education.