Data calls

Japan is a hugely technology-advanced country, wondering if there are any ways to make calls using mobile data instead of phone minutes? (e.g. any apps)

A few of the companies or hotels I will need to contact during my trip only has a local phone number, if I can call them using my mobile data with prepaid wifi then I do not need to pay extra.

I put credit on skype and use for calls - is that an option for you?

I make voip calls with Line as my default (I can make regular calls too, but Line works very well).
There are lots of apps - I have also used skype, facebook, , whatsapp (since deleted - lousy terms of use), and none of these are country specific. I also know there are things like facetime and many of these options provide video not just voice.
Because these are not Japan specif, so not sure about the question unless you come from a country with unreliable networks.