Nakajima Racing driver Yamamoto set the quickest time of the two-day test on the afternoon session of the opening day, posting a 1m21.897s to outpace nearest rival Tadasuke Makino by 0.112s, also topping the second day.
Ren Sato completed an encouraging test for the Nakajima squad with the third-fastest time on the first day and overall.
The team's strong speed follows a disappointing first half of the season for both drivers, with Yamamoto's fourth-place finish in the opening round of the season at Fuji the high point of the campaign so far.
Sato sits eighth in the standings with a best finish of sixth in the same race, while Yamamoto is 11th, having only scored points on one other occasion since the curtain-raiser with ninth at Autopolis.
Speaking after topping the opening day, Yamamoto said that the Nakajima squad has yet to fully understand why he was able to show such strong pace after a difficult first half of the season.
"We spent time working on things we wouldn't normally do during race week, but honestly, it wasn't good," said Yamamoto.
"At the end of the session, I was actually surprised how much grip there was and I was able to set a good time, but why it was so good is something we have to analyse. It wasn't a time that I set with confidence.
"Also, not everyone was using OTS (Overtake System) or new tyres, so it's hard to evaluate. But I want to understand why I was able to set such a good time and make use of this for the second half of the season."
Pressed for more details on his issues so far this season, Yamamoto replied: "Basically, I've never been able to feel enough grip. We're not sure if that's because of the aerodynamics or the mechanical side.
"If we understood that, we could work on it during race week, but we don't know the current situation, so we are trying to find the cause."
Nakajima team director Takuya Izawa, who took over the role at the start of the year, struck a more upbeat note when asked about the speed of the team's cars, saying it could be a result of set-up changes made in the previous round at Sugo.
"Since the start of the season we have been struggling, but because we changed the set-up at Sugo and this test has gone well, I feel like what we are doing is moving in the right direction," said Izawa.
"We have changed the way we set up the cars. We can't keep going on as we are without trying things, so we made quite a few big changes. We tested them in a rush at Sugo, so we wanted to try them here at Fuji to see how they would work.
"Setting fast times is no doubt a positive thing, so I want to make use of that in the remaining races."
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