If you can find a passenger transatlantic ship, then you can do it the longer way, but I have no idea how much that would cost.

Here's an article in French (try Google translate) about travel between Europe and Japan by train and ship, it seems to cost in the ballpark of 2,000 euros.

Is your medical issue with flying related to the pressure, or the motion? If it's the motion, sea travel may not be much better. If it's pressure, you may have an additional constraint that you can't travel by road or rail over high mountains.

@fkraiem As far as I'm aware, the only scheduled passenger liner (i.e., not cruise ships) service across the Atlantic is on the Cunard ships. And it's expensive. Looking into travelling on a freighter across the Pacific would make more sense: container ships travel back and forth between Japan and the west coast of the US.

Is using a container ship even a thing? I didn't you could do that. It's not motion sickness, it's just my inner ear does not keep atmospheric pressure like it should. I love the water and I'm a part time ship captain, so that would be ideal.

@NateEldredge This is indeed worth bearing in mind. The highest section of the US Interstate road system is in Colorado and is over 11,000ft in altitude. Aircraft must be pressurized to the equivalent of below 8,000ft and it seems that most are actually around 6,000-6,500ft. So, if the asker needs to cross the Rockies, avoiding I-70 is a good move. Having said that, perhaps the problem is the rather rapid changes in air pressure in a plane; driving leads to much lower climb rates.

@cloudnyn3 See, for example, this question. BTW, ironic username for somebody who doesn't like being in the air. :-)

@DavidRicherby You literally described that perfectly.

There are planes (mainly business jets) which offer a sea-level cabin altitude all the way to cruise, but again you get into the cost problem.

@DavidRicherby You should use that as an answer. I will approve and thumbs up it. That was definitely very useful information and thank for the link to the question.

@cloudnyn3: Another option would be simply to call the local office of some shipping lines and ask whether their ships are set up to take passengers and how you'd go about booking. They may require you to go through an agency to handle insurance, billing and general hand-holding, but they should be able to direct you to an agency they're working with. They'll probably be less likely to bite you if you phrase it as a practical problem of moving yourself from point A to B under medical constraints, than if you sound like you have romantic ideas about ocean travel you want to live out. :-)

@HenningMakholm I don't think so, they are used to sell trips to people who have romantic ideas about ocean travel but they certainly don't want anybody with a medical condition as it's a big risk for them (freighter travel agents typically require a certificate from a GP…)

Note that motion (and motion sickness) is supposed to be noticeably stronger on a cargo ship, as it's not designed for comfort but for maximum efficiency (fuel consumption/amount of cargo).

Given that other people have put far more effort into their answers than I've put into mine, I'd suggest that you accept one of the more detailed answers instead. (You can change your mind about the accepted answer any time.)

wouldn't it be easier to wear some kind of ear protection that can keep it pressurised?

There might be some transatlantic ships (to be verified) from eastern coast of the USA to Europe. Then you can get by train to Moscow, take the Transsiberian railroad (7 days in a train, yay!) to Vladivistok, finally, a ferry from Vladivostok to Japan. Such a voyage would take at least 10 days of trains + a transatlantic trip + a ferry to Japan.

@JamesRyan For the pressure ratio from sea level to 8,000 ft (airliner cabin altitude,) you'd likely need something resembling a space suit and it seems unlikely you'd be allowed to wear it on board (not to mention the cost involved.)

@reirab thats actually complete nonsense. The pressure difference is not that great and far less than divers experience where protective equipment for this problem already exists. The cost is likely to be way way less than travelling by sea.

@JamesRyan The problem is completely opposite that of diving and diving suits also don't maintain sea level pressure. If your intent is to maintain sea level air pressure in the ears and sinuses, you'd need a fully sealed pressure suit that's capable of maintaining around 4 psi outward pressure (and permission to wear and operate it aboard an airliner.) It's quite doubtful that the cost would be less than the $2,000 of a trans-Pac cruise, especially after factoring in the cost of the flight.