As well as a strict training roster, the team had benefited from a good balance of Japanase and foreign players, he said.
Thompson - Japan could reach quarter-finals
"It's all well and good having a team full of Japanese homegrown talent and building that, but you really do need those foreign guys that come from those established countries, not only to play well but to teach new guys coming through."
However, he said Thursday morning's game against Scotland could be different as the team had lost the element of surprise - but would also have gained a lot of confidence from the win over South Africa.
"They'll be full of confidence but the Scots will see it coming, so should be a good game."
With their improved performance in the scrum and the set piece, Thompson said he believed Japan could reach the quarter finals.
"When they can get away with that they can play to their strengths, they can move the ball, they can play to the intensity and pace and skill level and hopefully run around these big teams.
"What an occasion it'd be for the Japanese to get in to the knockout stage of the tournament - and with the World Cup being here in 2019 it's something that world rugby needs."
- nzherald.co.nz