The 29-year-old Australian was 13th overall in the heats with 54.35sec, 2.22 off Japanese leader Kosuke Hagino, after also missing the 100m freestyle and 100m individual medley finals on Tuesday.
It follows a disappointing return to action for the five-time Olympic champion last weekend in Singapore, when he finished way out of the medals in his first competition in five years.
'Thorpedo' will also compete in Tokyo this weekend as he builds towards Australia's Olympic trials in March, where he will bid to set up a London 2012 match-up with American superstar Michael Phelps.
"If I get to the end of Tokyo and I'm not swimming faster I am going to be very frustrated and I'll be quite annoyed, because I expect this of myself at the moment," he said after his races in Singapore.
Thorpe announced his comeback in February and has been training in Switzerland under renowned coach Gennadi Touretski.
He collected five Olympic gold medals in 2000 and 2004 along with 11 world titles before quitting in 2006 aged just 24, citing a lack of motivation.