Georgina Houghton, 33, from Arlesey, Beds, acted quickly as Colby, seven, had all the classic symptoms of the lethal brain bug, including a terrible headache and raging temperature.
The mum-of-four rang NHS Direct for advice and was told to take Colby to A&E immediately.
Georgina and her husband Gavin, 34, were relieved when it turned out that Colby had been struck down by a virus instead of potentially deadly meningitis.
But the couple were outraged to get a letter days later from their local medical centre - reprimanding them for taking Colby to Lister Hospital, Stevenage, Herts, rather than their GP.
"I was absolutely furious," said Georgina. "We kept Colby at home for as long as we could, but we were told to take him in. He always has the energy to get up and play, but he didn't get out of bed and all he wanted to do was sleep. We were really worried.
"If a kid is so ill they don't want to watch TV or play with their toys, you know something is wrong."
To add insult to injury, the ticking off from Arlesey Medical Centre was even addressed to little Colby - although he did not open it.
The little boy has now recovered but Georgina is worried about using A&E in the future:
"We've spoken to people since, and they said now they wouldn't dare go. This sort of thing needs to be stopped - it's putting people's lives at risk. People shouldn't feel like they can't take children there, it shouldn't be like that.
"It's irresponsible. Most people who go to A&E hope to be reassured - they don't want it to be the worst case scenario. We were so relieved when we found out it wasn't meningitis."
Part of the letter to the Houghtons read: "We have received a letter from A&E regarding your recent attendance. It appears that you attended A&E about a problem that would have been best dealt with by a GP.
"A&E is for life-threatening conditions such as a heart attack or stroke and for the care of people who show symptoms of serious illness or who are badly injured."
Today Bedfordshire Clinical Commissioning Group, a new umbrella organisation responsible for 55 local GP practices, said the GP surgery had not been aware of advice given by NHS Direct.
A spokesman said: "It's current practice for some GP surgeries to write to their patients advising them of the importance of using their A&E departments for emergencies only and to promote the use of their GP service or the local out-of-hours GP service for non-emergencies.
"We very much regret if the letter caused distress but it was intended to help the family make the right choice about the service they need to ensure they receive the best possible health care in the future."
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