Read page 38 in this guide: http://www.uusyrityskeskus.fi/sites/uus ... 13_web.pdf
The relief is not given automatically: you have to apply for it when you file your tax return (which is right now if you are on an annual return basis). You can do the calculation yourself and deduct the relief from the VAT you submit when you make your bank transfer but make sure you get the numbers right!!! If in any doubt call the Tax Office directly. (Disclaimer: it's not my fault if you get the numbers wrong.)
If you have a bookkeeper, then it might be a good idea to double check that "lower limit relief" has been applied for.
