Thorpe, winner of five Olympic golds, finished third in his heat with a time of 54.09 in Singapore to rank 11th overall and outside the top eight qualifiers for the finals.
"I came here expecting to get absolutely hammered in races and I knew it was going to happen and anyone who didn't think that was going to happen didn't have this in perspective," Thorpe said.
"I was quite annoyed with myself this morning with my time and things like that. Racing for me is tough. It is really easy for me to train and do whatever I am asked. It is going to be about getting back in tune with competition and being able to do it well."
Thorpe was quick out of the blocks in lane six but lost ground in the second and third legs of the short course race with Australian team mate Chris Wright winning the heat with a time of 52.09.
"I would have liked to have made the final in that one," Thorpe said. "I didn't go hard where I should have and fell into an awkward kind of technique.
"I'm disappointed because I thought I would be a little bit faster this morning and I'm also disappointed as I thought technically some things would have been better.
"I have to have a kind of reality check of where I am as opposed to how I feel I'm training. I'm happy with the progression I am making."
It was the second day back in competition after coming out of retirement for Thorpe, who finished seventh in the final of the 100m individual medley on Friday.
Although the butterfly and individual medley are unfamiliar races for the lanky Sydney-born freestyle specialist, expectations are extremely high that the Australian can add to his huge medal haul in London next year.
"Thorpedo", with his huge-flipper like feet, had attracted few spectators at the Singapore Sports School on Saturday morning with many fans presuming he would qualify for the finals.
"I think a lot of people underestimated the complexity of swimming," said Thorpe, who also won three silvers and a bronze at the 2000 and 2004 Games along with 11 world championship titles.
"I told people if I was to start swimming again it would take me three years to get back to where I was and it may take that long - I'm planning on it not taking that long. I'm trying to fast track."
Thorpe, who will attempt to make the Australian Olympic team at the trials in Adelaide in March, races in Beijing on Tuesday and then Tokyo (November 12-13) for two more World Cup meetings and said things had to improve.
"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."
His coach, Gennadi Touretski, said that there was a chance that Thorpe, who regularly smashed world records in his pomp, could swim his favoured freestyle.
"It might be in Tokyo, it is up to the situation whether he will feel comfortable with this race."
South Africa's Chad Le Clos won the final with a time of 50.63 seconds, his third victory of the night after he also claimed the 200m freestyle and 200m individual medley.
There were Australian victories for David McKeon (1500m Freestyle) and Christian Sprenger (100m Breaststroke) while Jeremy Stravius of France won the 50m backstroke, China's Zhiwu Lu claimed the 50m freestyle and Omar Pinzon from Colombia won the 200m backstroke.
Australia dominated the women's events, winning five of the eight finals on day two of the meeting.
McKeon's sister Emma won the 100m freestyle, Leiston Pickett captured the 50m breaststoke, Rachel Goh triumphed in the 100m backstroke, Blair Evans prevailed in the 400m freestyle and Olivia Halicek claimed the 100m individual medley.
There were also wins for Sweden's Therese Alshammar in the 50m fly, Miyu Otsuka of Japan in the 400m individual medley and Korea's Hye Ra Choi in the 200m fly.