Freire is a three-time world champion
Spaniard Oscar Freire and New Zealand's Julian Dean were both hit by pellets from an air gun during Friday's 13th stage of the Tour de France.
Rabobank's Freire had a pellet removed from his leg while Dean, who rides for Garmin-Slipstream, was hit on a finger.
"Oscar heard three shots and then felt a sting. A small shot was removed," said a Rabobank team spokesman.
"Julian has a minor injury on his finger, but he was able to finish," said Garmin spokeswoman Marya Pongrace.
French police are hunting two teenagers and have contacted both riders for their accounts of the events.
"This is the work of a pistol or an air gun," Colmar prosecutor Pascal Schulz said.
"According to one of the riders, [the shots] would have been the work of two youths aged between 16 and 17 who were hiding behind a tree."
Both riders started Saturday's 199km stage to Besancon.
"It's past now, it's forgotten," Freire said on Saturday.
I just heard shots and my leg hurt as if I'd been stung by a bee
"I still have a little bit of pain but the team doctor told me it would not be any worse than the pain of riding for 200 kms.
"I suppose this is the sort of thing that can happen on a race which takes place in the middle of the public," he added.
Freire was hit in the thigh while Dean was struck on the left index finger.
"I just heard shots and my leg hurt as if I'd been stung by a bee," Dean said.
"I'm always thinking about my safety up here on the roads but I don't have to think too much about it, I'll just try to stay focused on the race."
The two teams filed a complaint over the incident.
An investigation has been opened into a possible crime of voluntary violence with a firearm - an offence that carries a three-year prison sentence and a fine of 45,000 euros.
The 200km stage from Vittel to Colmarstage was won by Cervelo rider Heinrich Haussler, the first stage win of his career.
Italian Rinaldo Nocentini continues to wear the leader's yellow jersey.