CLEARWATER, Fla. - The Phillies reportedly accused two college draft picks who did not sign contracts last summer of potential NCAA violations, a decision that could affect the team's future negotiations with amateur talent.

Phillies general manager Ruben Amaro Jr. confirmed Thursday that an NCAA investigation was ongoing, as first reported by Baseball America, but he would not comment. He referred inquiries to Marti Wolever, the team's assistant general manager in charge of amateur scouting. Wolever was not available for comment.

At issue is the eligibility of Ben Wetzler, a senior lefthander at Oregon State University, who is suspended pending the outcome of the investigation. The Phillies drafted him in the fifth round of last year's draft (151st overall) but could not reach an agreement. Wetzler returned to school as the ace for the No. 2 team in the country until the NCAA intervened. The Beavers' season started Feb. 14 without Wetzler.

A source said the Phillies offered Wetzler a signing bonus above the suggested $315,200.

The Phillies, according to Baseball America, believed Wetzler violated the NCAA's rules against retaining an agent. It is standard for amateur players to rely on an adviser - someone who does not formally represent them - during negotiations with major-league clubs. A player forfeits his amateur status when he hires an agent. Advisers are not permitted to directly negotiate with teams.

Teams that do not sign their top picks rarely report such violations, according to Baseball America, the well-regarded industry publication. College players are not expected to engage on their own in contract negotiations with billion-dollar companies.

Jason Monda, an outfielder from Washington State drafted in the sixth round, also did not sign with the Phillies and was reported. Monda was cleared of wrongdoing by the NCAA last week, Baseball America reported.

Wolever was critical of Monda immediately after June's draft.

"He agreed to the draft and then just changed his mind; he just decided to go back to school," Wolever said at the time.

The initial backlash in the amateur-scouting community was strong, although the entire story remained a mystery because the Phillies remained quiet. A rival team's official called the Phillies' actions "petty." These reportings to the NCAA could sway college coaches to advise their future drafted juniors against negotiating with the Phillies.

The Phillies have publicized their disagreements with previous unsigned picks. Alec Rash, a second-round pick in 2012, enrolled at the University of Missouri instead of signing with the Phillies. Wolever told The Inquirer in July 2012 that Rash "hasn't performed like a player deserving of more than the slot" bonus.

"He seemed to have a different price for every team," Wolever said. "It changed depending on the day."

Extra bases. Ryan Howard was excused from Thursday's workout for personal reasons. He will return Friday. . . . Outfield prospect Aaron Altherr is limited in camp because of a nagging right wrist injury suffered in the fall. He is not throwing or swinging a bat. . . . Baseball America named Maikel Franco the 17th best prospect in baseball. Jesse Biddle (No. 71) and J.P. Crawford (78) also were ranked in the top 100 prospects.