The Japanese Customs website says that a visitor can bring 3 bottles of alcoholic beverages each about 760 ml in size. Am I allowed to bring one or two 1-litre bottles of alcohol into the country?
Yes. The 3 x 0.76 litres is to be taken as an overall quantity. You're allowed to bring in 2.28 litres, give or take. I used to go to Japan every six weeks, and usually took with me this much (or sometimes more, ssshhhh), in 10-cl bottles (tasting samples for my clients).
When the Customs officers inspected my bags (which happens a lot, as Japanese Customs are quite diligent), I would show the bottles before they asked, and they would count the bottles, and multiply, nodding to themselves. Then they would send me on my way.
I also brought a couple of times litre-sized bottles without any issue either.