Thomas responded in a conference call with reporters to allegations made Sunday by Cvijanovic that Beckman bullied and mistreated players amid Illinois' mishandling of injuries suffered by Cvijanovic in 2013 and 2014.
"The feedback I get from the players and our players' families is that these coaches genuinely care for them and treat them like their own children," said Thomas, who hired Beckman in 2011.
Thomas said he considers the allegations made by Cvijanovic as "very serious." The athletic director said his department would conduct a review of the matter in cooperation with the chancellor's office.
"We will have a follow-up," Thomas said. "We will review, and the timeline and who's to be involved will be determined very soon."
Cvijanovic, 22, went public Sunday on Twitter and in subsequent interviews, saying Beckman ignored the player's signs of mental illness, which led Cvijanovic to quit the team late last season.
Thomas said he was unaware of Cvijanovic's grievances until Sunday.
Ramogi Huma, president of the National College Players Association, on Tuesday sent a letter to Illinois chancellor Phyllis Wise, requesting an independent investigation of the claims and a public release of the findings.
Wise will receive the letter Wednesday, Huma said. He asked for a response from the chancellor by Friday.
Cvijanovic contacted the NCPA, a non-profit advocacy group founded in 2001 to serve on behalf of college athletes, last week, Huma said.
"We have some concerns," said Huma, a former UCLA linebacker who also leads the College Athletes Players Association. "These are very serious accusations, and an internal, secretive review is not going to cut it."
Set to graduate this month from Illinois and a starter in 33 games in four seasons, Cvijanovic said he spoke out because other players -- at Illinois and elsewhere -- are afraid to do it. Simon's brother, Peter Cvijanovic, who has Type 1 diabetes, recently left the Illini after one season, accepting a medical-hardship scholarship. He lost 40 pounds at the school, said Frank Cvijanovic, Peter and Simon's father, because Illinois coaches and staff mismanaged his diet and prevented him from properly handling his insulin intake.
"It's really just ridiculous," Frank Cvijanovic said. "[Simon] is a kid who's been looking to play in the NFL since he was 8 years old. Now that this has happened, he's just been filled with anxiety -- almost an identity crisis."
The Illinois medical staff documents all interactions with student-athletes, Thomas said.
According to Cvijanovic, doctors withheld information about the amount of meniscus removed from his left knee in a December 2013 procedure. Then after he started nine games as a senior and suffered a labrum tear in his left shoulder on Nov. 1 against Ohio State, coaches urged him to play through the injury.
The Cvijanovic brothers developed mental-health issues, Simon said, as a result of their medical problems and the staff's neglect. Prior to the knee surgery, Simon Cvijanovic said he had experienced no symptoms of mental illness.
Players at Illinois were berated and called derogatory names by Beckman for sitting out of practice, Simon Cvijanovic said. He said Beckman threatened to discredit him with NFL scouts for missing practice time with injury.
Thomas said he was unable to comment on a specific medical case. He said he has never heard of coaches punishing players for injuries.
"I can tell you we are confident that we're following all appropriate policies and procedures for our sports medicine program," Thomas said. "The No. 1 priority, has been and always will be, the health and well-being of our student-athletes."
Since Cvijanovic's accusations became public, Thomas said he has heard from parents of players in support of Beckman. The Illinois administrators visit each year with the majority of players who leave the program.
"The feedback from our student-athlete exit interviews don't correspond with what we're hearing from Simon," Thomas said.
"It's been very positive from the kids and the families. They talk a lot about the family atmosphere. They talk about the culture. They talk about the caring of our coaches as it relates to their well-being."
Illini AD to review player allegations vs. Beckman
ESPN Big Ten reporter Mitch Sherman breaks down Illinois athletic director Mike Thomas' plans to review allegations of bullying and mistreating players leveled against coach Tim Beckman.