The Houston Astros failed to sign the first pick in this year's draft, San Diego high school left-hander Brady Aiken, before Friday's deadline.
The head of the players' association said the union is working with the pitcher and his advisers to explore "all legal options."
Aiken originally was offered a deal with a $6.5-million signing bonus by the Astros, a person familiar with the negotiations said earlier this week, speaking on condition of anonymity because no statements were authorized. But the club expressed a concern regarding Aiken's elbow ligament and lowered the offer, the person said.
The union is also concerned with Houston's handling of the negotiations with fifth-round pick Jacob Nix. The right-hander from Los Alamitos, California, didn't sign either.
"Today, two young men should be one step closer to realizing their dreams of becoming Major League ballplayers," union head Tony Clark said in a statement. "Because of the actions of the Houston Astros, they are not. The MLBPA, the players and their advisers are exploring all legal options."
The Astros insisted in a statement their offer to Aiken "was extremely fair considering all the factors involved in this case."
"As always, we approached these negotiations in good faith and with the best interests of the Astros organization in mind, both short-term and long-term," the team said.