There are good supplies of antibiotics to treat strep A and stock can be moved around if there are issues in some areas, Health Secretary Steve Barclay has told the BBC.
But pharmacies are worried about patchy supply caused by rising demand for penicillin and amoxicillin.
These medicines are used to treat cases of strep A and scarlet fever, which are higher than usual around the UK.
Nine children have died with rare but severe bacterial strep A infections.
Health experts say parents and doctors need to be vigilant and alert to the symptoms of infection.
GPs have been advised to prescribe antibiotics for children who may have worsening symptoms linked to strep A.
Strep A can look like a number of different conditions, and is mild in most cases, causing a sore throat or skin infection which is easily treated with antibiotics.
But it can develop into scarlet fever and, very rarely, into invasive group-A streptococcal infection (iGAS) which can be extremely serious.
Schools with a number of cases of strep A or scarlet fever could be given antibiotics to hand out to pupils in order to prevent further spread of the bacteria.
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This is prompting concern from pharmacists that stock of antibiotics could run low unless there is some planning around supply.
Mr Barclay told BBC Breakfast: "We have very regular contact with the medical suppliers, and the manufacturers have said they don't have concern in terms of supply at the moment.
"It is always the case that if you have a particular surge in one or two GPs then the response suppliers look at warehouse depots and how they move their stock around.
"What the suppliers have said to us is they do have good levels of supply, and that is not a concern at the moment, and where there are particular issues with GPs, then they will move stock around accordingly."
However, the National Pharmacy Association (NPA) says pharmacies are having to "work very hard to obtain stocks of these antibiotics and some lines are unavailable".
It says there has been a spike in demand for some antibiotics, including those used to treat strep A in children.
"We have been advised by wholesalers that most lines will be replenished soon, but we cannot say exactly when that will be," the NPA said.
Pharmacists said they would work with local GPs to help people get the medicines they need as quickly as possible, but that could require a change of prescription.
The Association of Independent Multiple Pharmacies, which represents 4,000 pharmacies, says the supply of antibiotic medicines in oral liquid form (for children) from wholesalers is "patchy".
It says pharmacies are experiencing supply issues from all wholesalers, and it puts this down to a big rise in the number of prescriptions for antibiotics.
What should parents do?
Trust your judgement if your child seems seriously unwell.
Contact your local surgery if they:
are getting worse
are eating much less than normal
show signs of dehydration, such as a dry nappy for 12 hours
have a temperature of 39C or higher, or 38C if under three months old
are a baby and feel hotter than usual when you touch their back or chest or sweaty
are very tired or irritable
Call 999 or go to an accident-and-emergency unit if:
they are having difficulty breathing - you may notice grunting noises or their stomach sucking under their ribs
they are pausing when they breathe
their skin, tongue or lips are blue
they are floppy and will not wake up or stay awake