The Spaniard tested the engine at Friday practice in Malaysia before reverting to an older-spec unit for the remainder of the weekend.
He got the green light to use the new engine this weekend in Japan, but he and Button have struggled for performance in Honda’s home race, reports Motor1.
Alonso qualified down in 15th position on Saturday, two places ahead of Button, who was unable to reach Q2.
Alonso said said upgraded engine has just given him more reliability but not more power.
“The improved engine lasts more kilometres, but it has the same power, and Jenson and I are as quick on the straight,” said Alonso.
“What we are trying is to not have more penalties the rest of the weekends.”
“We haven’t been quick all weekend, and we need to understand why. It’s going to be a difficult race starting from the back.”
When asked if McLaren was surprised by the lack of performance this weekend, Alonso said: “A little bit, yes. We are not happy with the performance today.
“We didn’t perform as we had hoped, especially here in the home Grand Prix for Honda. But it is the way it is.”
Alonso admitted he was not expecting to make much progress in tomorrow’s race, and was hoping for rain to give him a chance to shine.
“You never know how qualifying will go until you are in it, but being 15th and 17th is not the ideal position for the McLarens. After a few Grands Prix, where we got used to be in Q3 or fighting to be in Q3, we are lower than we thought we’d be.
“We have to try to improve for tomorrow. We haven’t been very fast all weekend, so it’s not like tomorrow we’ll make up many places by surprise, unless it rains or something strange happens.
“So let’s hope we find something tomorrow or the weather helps, because we are slower than expected this weekend.”