On Friday, Mexico's attorney general, Jesus Murillo Karam, said three gang members confessed to killing, burning and burying the bodies of 43 students who went missing on 26 September after clashing with police in Iguala, Guerrero.
On Sunday night, Crunch Mexico, a twitter account dedicated to Nestle's chocolate bar, poked fun at the tragedy, tweeting: "A los de Ayotzinapa les dieron Crunch".
The phrase plays on a slang term used when someone is beaten up and loosely translates into "Those from Ayotzinapa were crushed".
The tweet sparked calls for a boycott of Nestle products on social media and was dismissed as "insensitive" and "tasteless".
Nestle has taken the tweet down and issued an apology vowing to investigate the incident but refused to elaborate on whether the account had been hacked.
A spokesman added: "We have apologised for this completely unacceptable tweet which is entirely contrary to the values of our company.
"We deeply regret any distress it may have caused. We understand and share the public's concern about this post. We take this matter extremely seriously."