But he ground out a win.
The top seed beat Ville Lang of Finland 21-8, 14-21, 21-11 in 51 tense minutes to scrape into the last 16 and send a wave of relief through Malaysia.
Chong Wei was Malaysia's greatest hope for a first Olympic gold medal, and the fear they held that the Beijing silver medallist might not be fit in time for London was revealed by chef de mission Tan Sri Ahmad Sarji, who said only half-jokingly last week that Chong Wei's fitness was a state secret.
Now the badminton world knows Chong Wei looks vulnerable, though he also worked out some considerable rust. The draw allowed him two extra days to finish off an intense rehabilitation, and he won't play again until Wednesday, likely against the tough Simon Santoso of Indonesia.
"This is my first match. The second will be better and the next one better," Chong Wei said.
Meanwhile, his archrival and the defending champion, Lin Dan of China, eased through his opener against Scott Evans of Ireland 21-8, 21-14. Lin's leading countrywomen, world champion Wang Yihan and No. 2-seeded Wang Xin, were equally unruffled.
The only upsets were inflicted on the No. 8 seeds in both draws. Kenichi Tago, the only Japanese man to reach the All England Open final in the last 45 years, lost to Niluka Karunaratne of Sri Lanka 21-18, 21-16 and Sung Ji-hyun of South Korea lost to Yip Pui Yin of Hong Kong 21-18, 23-21 just a day after her 22nd birthday.
"I don't feel so happy anymore," Sung said.
Chong Wei didn't look so good, either, after he ruined a bright start and played with less conviction and more errors in the second game. Lang won it 21-14, the first time he'd won more than 11 points in a game off Chong Wei.
Chong Wei won a morale-boosting 50-stroke rally for 2-2 in the deciding game, and as Lang began to pile up errors, Chong Wei accelerated from 11-11 by winning the last 10 points, finishing with a cross-court smash that Lang didn't even twitch for.
Lin opened his bid to become the first man to successfully retain the Olympic singles title when he outclassed Evans, conceding nine points fewer than when he beat Evans en route to winning the world title in the same Wembley Arena last year.
"I've been preparing since 2008 so I have put a lot into this. So I am very nervous. But if you want good results, it's normal to be nervous," Lin said.
Karunaratne showed no nerves in dispatching a lacklustre Tago, and when it was over he pointed to his father and mentor Louie in the stands and thumped his heart three times.
"This is the biggest win in the history of Sri Lanka badminton," Karunaratne said with pride.
It was no surprise to him as he's in the best form of his life — has been since October when he began travelling to qualify for the Olympics at his third attempt. He won his first international title on his father's birthday in Puerto Rico last November, and picked up more titles in Miami, Wales, Uganda and Iran. His ranking shot up from the 160s to a Sri Lanka-best ever 47.
Joining him in the last 16 were No. 4 Chen Jin of China and No. 5 Peter Gade of Denmark.
In women's group action, Wang Yihan opened her first Olympics with a 21-8, 21-16 win over Michele Li of Canada, and Wang Xin beat Rena Wang of the United States 21-8, 21-6.
Also advancing from group play were No. 4 Saina Nehwal of India and No. 6 Juliane Schenk of Germany.