Guillen said he worked with Angel Presinal "for a very long time" but that the regimen never included performance-enhancing drugs.
"I never saw an injection," Guillen said. "He never asked me about steroids or anything."
Guillen said he has not employed Presinal since 2004 and doesn't plan to work with him again in the near future. He said Major League Baseball never told him to avoid working with Presinal.
"But he is a great friend of mine," he said. "He's one of the nicest guys who I ever met or worked with."
"We just did exercises," said Santana, according to the Los Angeles Times.
"He motivates you, he likes to work hard. He's like me, he doesn't like to lose."
Presinal, then training former slugger Juan Gonzalez, was questioned by Canadian Border Service officers in 2001 about steroids and syringes in an unmarked duffel bag, according to the Mitchell report. Presinal and Gonzalez both denied owning the bag.
Guillen was suspended in December 2007 following media reports linking him to performance-enhancing drugs. The 15-day penalty was lifted as all players implicated in the Mitchell report were given amnesty.
Guillen has been hampered by injuries this spring. While an ingrown nail on his right big toe has slowed him for a few days, a shoulder problem was revealed before Saturday's workout.
"He's got a sore shoulder," manager Trey Hillman said. "So we're going to back him down from swinging and throwing for the next couple of days. With the toe, it's just a matter of how quickly his body heals. That is still limiting him as far as running."
Guillen was allowed to stretch and participate in some defensive drills, but then was sent to the trainer's room for treatment.
"We want to try and get that [shoulder] settled down," Hillman said. "When it's one of your players that is planning on playing in the WBC, we want to send him off healthy as possible."
Guillen, who led the Royals with 20 homers and 97 RBIs last season, has said he would not play for the Dominican Republic in the World Baseball Classic unless he is 100 percent healthy.
Information from The Associated Press was used in this report.