Kirwan's men ran in tries from Kensuke Hatakeyama, Michael Leitch and Alisi Tupuailei, but also conceded three tries as Vili Ma'afu, Lua Lokotui and Fetu'u Vainikolo crossed for Tonga, with 16 points from Kurt Morath sealing the South Sea Islanders' win.
And former New Zealand wing Kirwan, a World Cup winner in 1987, admitted losing the battle of the breakdown had been vital.
He told ITV4: "I am very disappointed. They put incredible pressure on us and were very physical over the ball. We had too many errors and turnovers.
"The breakdown was key. They were very physical and very hard. There were 145 rucks in the game and if you can't dominate there you will struggle.
"There was too much pressure at the ruck and we couldn't get our rhythm, couldn't run around the park.
"We wanted to move them around and get up to seven or eight rucks (in attack). We felt at half-time when we hung on to the ball for four or five rucks we were scoring tries and making breaks."
The defeat was Japan's third from their three games in the tournament, but Kirwan is confident they can bounce back in time for their final pool clash with Canada.
"If we can hang on to the ball longer we can put teams under pressure," he said. "Our errors came from their pressure at the ruck. Fix that up and we'll be fine."
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