The two-time F1 world champion was heard on team radio describing the pace deficit to his rivals as “embarrassing”, while likening his Honda power unit to a “GP2 engine” on his way to an 11th place finish at Suzuka.
Alonso's comments come following a period of meetings between McLaren and Honda as the pair aim to improve the struggling partnership for next season.
The driver was somewhat more reserved in his judgement of the McLaren-Honda package post-race, but was not shying away from his frustration.
“On the track there is not much to enjoy,” he said.
“When we are being overtaking like we are on the straights it's frustrating.
“You feel embarrassed a little bit because it is not possible that some of the guys overtake us like this because the package should be more competitive.
“Everyone knows the problems and we are working on the solutions for next year but we cannot hide from it.”
McLaren boss Ron Dennis said that Alonso's comments were ill-timed and not constructive, but stopped short of criticising the Spaniard.
“I didn't think he needed to make the comment, it wasn't particularly constructive,” Dennis told Sky F1.
“We are here in Japan, Suzuka, Honda's home track and we had the president of the Honda motor company, we had the head of R&D and the chief executive of Honda motors here.
“They are the three most senior people who are totality committed to winning a world championship.
“The curve is much steeper than anticipated but their aspirations are undiminished.
“He (Fernando) vents his frustrations in different ways. I wouldn't say its constructive but I'm not going to get to angry about it.
“My own personal professionalism is to put it to one side if I have got anything to say I will say it to Fernando. At the end of the day we know what we have got to do and we will get there.
“The drivers get relatively minimal interface with key management of Honda, maybe this is to make sure the message is heard by everybody.
“I do not condone it but I am not going to criticise our drivers because they are pretty frustrated. I will sort it behind closed doors.”
Sky F1 analyst and former grand prix winner Johnny Herbert was scathing of Alonso's comments, saying the driver's actions could destroy the relationship between McLaren and Honda.
The controversy comes in Alonso's first year back with McLaren after a tempestuous single season at the team in 2007.
“It is destroying,” said Herbert of Alonso's comments.
“We keep talking about the relationship with McLaren and Honda being a little bit brittle at the moment and then you get a driver going out there and saying all these things, that only feeds Honda to say ‘why are we involved in this'.
“For him, he's coming to the end of his career, he's got a couple of years left and then he'll be moving on, but of course this relationship is going to be carrying on.
“You don't want to destroy it for them for the good of yourself. It's selfish. You can't go out there I don't think and slag your team off.
“If you're not happy with the situation, bugger off,” he added bluntly. “Don't get involved with racing anymore.”