First off, I don't know medical Japanese, so I was sure to bring a note I had written earlier with all of my symptoms. The staff didn't speak English, though I'm not really close to a larger city, so that's to be expected.
Like most other medical offices I've been to in Japan, this clinic had walk ins for most of their working hours. New patients are required to do a brief questionnaire, mostly with typical questions you could expect anywhere (have you been pregnant, normal cycle length, why you're there today, etc).
I went on a Saturday, so the number of doctors was limited. There was a female doctor in obstetrics, and a male doctor in gynecology. There wasn't an option to request a female doctor as it was segregated by division, which... I was uncomfortable with at first. I suppose that if you make an appointment you may be able to request a specific doctor, but as this is the only ob/gyn in my area and Saturdays are the only day I can go, there wasn't really an option.
When I was called into the consultation room, I spoke with the doctor who was going to do the pap test. He was much friendlier than most doctors I've seen here, and he explained everything that he would do (though briefly).
I then had to go to an examination room, which had by far the most high tech gyno equipment I have ever seen. It was much smaller than what I was used to in the states, and there was a huge chair that looked like it was from a dentist's office. No idea if these are common anywhere, else but back home I'd only ever seen the table+stirrup set ups.
Anyway, the seat itself was short (it protruded maybe about 10 inches). Sit down, put legs into compartments that look like something from a massage chair. Doctor pushes a button and BAM! Chair goes back, the leg compartments spread everything open, and the bottom of the seat drops down so the doctor can check everything out. (Is this a normal thing?!) I was still pretty anxious, but there was a privacy screen, which made the fact that a male doctor was poking and prodding around a lot less uncomfortable.
There was no manual exam. I had mentioned my cramps, a few cysts and an irregular period, so they did a trans vag ultrasound to make sure that things were ok physically. It was pretty uneventful.
Then he did the pap test... Which was... I never like pap smears because they make me nauseous. The swabbing for BV and whatnot was barely noticeable, but it seemed like more was being done near my cervix than what they do in the States. I found out why when the doctor told me that they had put a tampon in to prevent bleeding.
This was the one problem I had. I figure it's just a big difference of medical culture, but I wasn't particularly happy about having a tampon shoved in me without having been asked. The last thing I really want right after having my cervix scraped is a wad of cotton being shoved in my vag. That said, it was pretty much the smallest tampon I have ever seen (it was only about 1.5 inches long and only about as big around as my pinky), so it wasn't as bad as removing a regular tampon when you're not on your period.
The trans vag and everything turned out ok, so they decided to do some blood tests (including a pregnancy test) to make sure that there isn't any other underlying reason for my recent problems. They also gave me two kinds of medicine that should help with my cramps, which is awesome since I'm running out of the naproxen that I brought. I get my test results next week, which is much faster than my doctor back home was with tests.
And to top it all off, with national insurance the cost was only about $60 for everything. The last time I went to a gynecologist back home, it was $100 just for the pap smear, plus about $60 for the appointment itself. Even without insurance, the cost of my appointment today would have only been about the same as a pap smear in America, so I'm pretty relieved that half of my pay this month didn't disappear after having so many different tests done.
TLDR: Gynecologists in Japan aren't any worse than they are anywhere else, and tests are super cheap if you're used to American medical costs. (Also, really cool chairs.)