"There is beginning to be dangerous discourse against vaccination" that is not supported by scientific evidence, said Health Minister Alfonso Alonso, adding that "it is irresponsible not to vaccinate", newspaper El Mundo reported.
Alonso's warning came after a six-year-old child who had not been vaccinated was admitted into hospital this week for contracting diphtheria - an illness that has not been seen in Spain since 1986.
Diphtheria is an infectious disease caused by the bacterium corynebacterium diphtheriae that usually affects young children and the elderly.
It is spread through the respiratory tract via coughing and sneezing and has a mortality rate of one in ten.
The childhood illness was eradicated in Spain almost 30 years ago thanks to routine vaccination programmes.
The boy is being treated at the Vall d'Hebron hospital in Barcelona and is reported to be in stable but serious condition. He first showed signs of the illness on May 25th when he presented flu-like symptoms including headache, sore throat and a fever.
Alonso declined to comment on why the child's parents did not have him vaccinated, but the minister did say that he hoped this case would help "raise awareness among parents that they have to safeguard the rights of the children and that this always must be above the interests of the few".
"If our children are protected, they will not have to be afraid of sicknesses that once were very grave and that today are practically unknown," he added.
Sources told newspaper El Pais that the boy's parents had decided not to vaccinate him. The newspaper also said that his mother is a physical therapist at a homeopathic clinic.
In the area where the boy is from in Olot near Girona, there is reported to be a common practice of parents choosing not to vaccinate for ideological reasons, choosing natural medicines because of their concerns about side effects of vaccines.
The Public Health Agency has said that it is administering preventative medication and booster vaccination to those who had close contact with the boy.