Hello ADHWGT
I strongly urge you to get tax advice from someone who is familiar with foreign income and foreign tax issues. The tax advice you received from that consultant is suspicious. Your overseas income is not taxable in Japan unless you are deemed a permanent resident for tax purposes, or unless the income is actually considered "Japan Source Income" (for a definition of Japan Source Income, please see the link below). I don't believe freelance reporting for a foreign newspaper while in Japan as a student would be considered Japan Source Income, and there is nothing in the definition that sounds like it fits your situation. So that income would only be taxable as Japan income in the event that you are deemed a permanent resident. Note that a permanent resident for tax purposes is not necessarily the same thing as a permanent resident for immigration purposes. To say another way, even if your visa is limited, you can be considered a permanent resident for tax purposes. In your case, if your first visit to Japan was in September 2012, you have not met the 5-year requirement for permanent residency. Therefore you are considered a Resident who is a "Non-permanent Resident" (see the definition of Residents on page 3 of the tax guide). As a Non-permanent resident you are obligated to
"pay income tax and special income tax for reconstruction with respect to any income which has its sources in Japan, any income which has its sources abroad and is paid in this country and remitted from abroad."
For a definition of foreign source income you can see the file below.
日本のカジノ税
It could be that your consultant is considering you a permanent resident (?), which to me sounds odd since you only arrived in September of 2012. Or, it could be that she is considering your income Japan Source Income, which also seems odd to me. And finally, her advice regarding the foreign tax credit has to be looked at with suspicion. The calculations required are not particularly complicated, and for a tax professional they are very ordinary calculations. Lastly, I do not know how much you make, but Japan allows fairly generous deductions. Given the potential deductions, and the potential for foreign tax credit, even in the unlikely case that your Swedish income was taxable, I would bet that the sum of your deductions and credits would bring any taxable income down to a very low number, if not zero.
Again, this is an area for experts, and you shouldn't rely on information from friends or anonymous guys on the internet ;-). But I do think your situation is not strange, is not taxable, and even if you wanted to be very conservative and declare it as if it were Japan Source Income, your taxable income would be very small indeed.