Astros general manager Jeff Luhnow issued a statement Friday following the announcement of the suspensions.
"We were disappointed to hear the news of these suspensions," he said. "The Astros fully support the Minor League Drug Prevention and Treatment Program. Our Minor League players undergo extensive drug prevention training, so it is very unfortunate when something like this occurs.
"Moving forward, we will continue to review our entire drug education and prevention program to identify opportunities to enhance it in order to prevent future violations."
Martinez, a first baseman who was a 36th-round Draft pick last year out of Florida International, was hitting .225 with 11 homers and 35 RBIs in 59 games for Class A Tri-City. Fernandez, a shortstop signed as a non-drafted free agent out of the Dominican Republic in 2009, was hitting .258 with seven homers and 28 RBIs in 16 games for the Gulf Coast League Astros. He played in seven games for Tri-City earlier this year.
Toney, a center fielder acquired along with left-handed pitcher Kevin Chapman from the Royals in the trade that sent Humberto Quintero and Jason Bourgeois to Kansas City in 2012, was hitting .219 with two homers, 12 RBIs and 13 stolen bases for Tri-City.
Brian McTaggart is a reporter for MLB.com and writes an MLBlog, Tag's Lines. Follow @brianmctaggart on Twitter. This story was not subject to the approval of Major League Baseball or its clubs.