An update on his condition was given by Spain's minister of health, Alfonso Alonso, on Monday night.
The six-year-old boy, who has now been identified only as Pau, is being treated in the intensive care unit of Vall d' Hebron hospital in Barcelona where his condition is described as "critical but stable".
"Pau would not have a chance without the excellent professional care he is getting," said the minister. "This case shows us many things, not least that it is important to trust in scientific evidence and not be influenced by other theories."
They are being kept in isolation along with their parents to prevent the infection spreading.
Pau, a resident of Olot near Girona, first showed symptoms on May 25th. His parents had chosen not to vaccinate him, a decision they said they had come to regret.
His mother and father admitted last week that they "feel terrible guilt" for not vaccinating their child and said they felt hoodwinked by the anti-vaccination movement that convinced them not to immunize their son.
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 last case being reported in 1986.
It was reported that the six-year-old had recently spent several days at a school camp, but no further cases have yet been detected.
The boy was said to be "responding well to treatment" but was still "in a serious condition" according to a spokesman at the hospital.
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The case has provoked furious debate in Spain over whether parents should be legally obliged to vaccinate their children.
It was widely reported that the parents of the six-year-old suffering from diphtheria had opted not to vaccinate him, part of a small but growing minority of parents against immunization because of their concerns about side effects of vaccines.