The Welshman crashed due to a parked police motorbike on stage nine and abandoned five days later with a sore knee and shoulder.
Since May 19, he has been recovering, training in Monaco and previewing Tour stages with Chris Froome.
“I don’t feel quite like the same as before the Giro,” Thomas told Cycling Weekly.
“In Trentino [Tour of the Alps ahead of the Giro], I felt like I was all prepared and ready to go, in Route du Sud [June 15 to 18], I was still on my way back up.
“It’s taken a while to heal up, I’ve healed up properly, but still have to do physio exercises and stuff. It’s definitely a different sort of run in to the Tour compared to the Giro.”
After Thomas worked for Froome’s three Tour de France wins, Sky gave him his first chance to start a Grand Tour as a leader. He and Mikel Landa led the Giro team, but both crashed in the police motorbike incident.
Landa recovered to win the Piancavallo summit finish stage and the mountains jersey and will work for Froome at the Tour this July.
“In the Giro, I was confident that I was feeling the best I had and ready to go,” Thomas said. “This time, I’m starting to get my way back up. I think once we get into the race it’ll be fine.”
If Thomas shows the fitness that he had leading to the Giro d’Italia, which included winning the Tour of the Alps, he could contend for the Tour overall.
Sky will keep him as its backup in case something happens with Froome over the three weeks, from July 1 to 23.
“I’m not sure, I think it’s a bit up in the air,” Thomas said of his Tour hopes. “I haven’t been feeling that great in the build up, I’m starting to feel better now, but it’s a bit of an unknown.
“Of course, having a few guys around Froome in the GC will help because a lot will be going on. This is definitely a racer’s sort of race, much can happen. Look at the Giro. So having those bodies around in the top-20 is always handy.”
Thomas will not race the Vuelta a España but said he would “love to” receive the leadership role and face the Giro d’Italia again in 2018.
“I still want to go back there for sure, have another go. I felt like my preparation went very well this year and I’d love to have another go, for sure.
“It’s hard just to lead the team in the first place in a team like Sky. It was a great opportunity this year but it didn’t quite happen.
“The form was there, though, and it gave me confidence that I know how to get into decent shape now.”