Manson was second-fastest of 40 rowers in the heats. His quarter-final time of 6 minutes 55.880 seconds was slightly quicker but still more than 15sec down on what he has produced.
Russian Vladislav Ryabcev was the fastest in the quarter-finals, with all the other big names advancing, including four-time world champion Ondrej Synek of the Czech Republic.
Elsewhere, Kiwi lightweight single sculler Matt Dunham also cruised into the semi-finals.
Dunham won his quarter-final easily from Hungarian Peter Galambos and clocked the fourth-quickest time overall.
The lightweight men face an intense schedule, with the semi-finals and final taking place on consecutive days.
Hannah Osborne is still afloat in the women's single sculls after placing second in her repechage behind Canada's Carling Zeeman.
Osborne, competing in her first senior international season, was third in her heat.
Earlier, the women's four became the first of New Zealand's 13 crews to lose any hope of winning a medal.
Jackie Gowler, Kirstyn Goodger, Beth Ross and Ellie Jeurissen were fourth in their repechage and will contest the B final.