Scotland lost the pre-World Cup friendly 1-0 on home turf, with fans jeering the players at the final whistle.
Clarke reacted afterwards: "Yep. I am disappointed. I’ve got to be honest.
"It’s just the modern way. It seems to be now that, if you lose a game, you get booed. You’ve just got to deal with it, but it disappoints me.
Japan substitute Junyo Ito struck for the visitors and Clarke also said: "There are a lot of things I can take from the game that were decent.
"We played against top-quality opposition, but we didn’t create enough in the final third of the pitch and that is something to look at. It is something we have spoken about often and we’ll keep trying to get better.
"First of all, you do have to look at the quality of the opposition. They are a top-class team and, towards the end, they were bringing on stronger and stronger players. I chose to go the opposite way because I had players who needed minutes on the pitch and also had to protect them.
"It’s just about keeping working at what we do. The end result is important. We spoke before the game about the fact our record in friendlies is not as good as it should be.
"I thought the performance, at times, was OK against a good team.
"It’s not a game you want to lose, but I thought there was enough in that game against the opposition we played against to feel positive about what we are trying to do.
"We have another tough game in Liverpool against Ivory Coast on Tuesday. I think some of my players look at me and ask what I’m doing, but I always try to pick difficult friendlies.
"We will try to get a positive result to carry us forward, but, if the performance is good and you can take things from it, you can carry that on too.
"We’ll have a look at the lads, but I would expect six or seven changes to the team as there are other things I want to look at."