Sion Bedwyr Evans, 41, of of Llanrug, and Garry Vaughan Roberts, 43, of Caernarfon, had faced 50 charges between them.
They were alleged to have happened at Canolfan Brynffynnon in Y Felinheli between September 2006 and March 2014.
The Crown Prosecution Service said the charges had been dropped after new information from the police.
Catrin Evans, head of the CPS Cymru-Wales Complex Casework Unit, said they had written to the court confirming the prosecution will offer no evidence against Mr Evans, who was acting head teacher at the unit, and his colleague.
Two members of staff at a Gwynedd education referral unit have had child cruelty charges against them dropped.