Alonso's criticisms came as he struggled to fend off other cars on the Suzuka straights, leaving him 11th at the chequered flag.
"There's not much to enjoy on track," said the Spaniard following the race. "Obviously it's frustrating how they overtake you on the straights and then you arrive at the corner and you see them braking late, making mistakes - you take the corner perfectly and you are recovering time and they just overtake you on the straights.
"Days like today you feel a bit embarrassed. It's not possible some guys overtake you like this - we should be more competitive. But this is the way it it and hopefully we can learn lessons from this kind of races.
"Both cars finished after a double DNF in Singapore, so on the positive side we improve our reliability and our weak points and we don't repeat errors like the gearbox overheating in Singapore."
Alonso reiterated his belief that McLaren-Honda are the team best placed to rival Mercedes in the long term, however, adding: "Definitely I can see [McLaren] are the only team that will challenge Mercedes in the near future. Right now its tough times, we don't have the toys to fight with them. The positive thing is that everyone knows the problems, we go deep into the solutions we need - but we cannot hide this is frustrating."
Jenson Button, who finished five places behind his team mate, added: "I can't do anything to keep other cars behind, they are so much faster on the straights. We are doing our best, we just have to keep heads down and focus. We're finding it tough as drivers, the team are finding it tough, but I think what is coming is positive - it's just going to hurt for the rest of the season."
Alonso and Button have claimed just four top-10 results between them this season, while this weekend represents only the fourth time both drivers have seen the chequered flag.