However, the agency has said there is no current evidence that a new strain is circulating and the rise in cases is most likely due to high amounts of circulating bacteria and increased social mixing.
Figures show that scarlet fever cases remain much higher than normal.
The UKHSA said cases usually show steepest rises in the New Year, but have increased sharply in recent weeks.
So far this season (from September 12 to December 4), there have been 6,601 cases of scarlet fever, more than twice as high as the 2,538 at the same point in the last comparably high season in 2017/2018.
Health Secretary Steve Barclay insisted on Wednesday that checks within the Department of Health have not revealed an issue with supply of the medicines.
However, the National Pharmacy Association has pointed to “blips” in the supply chain of liquid penicillin, while the Association of Independent Multiple Pharmacies said pharmacists across the country were struggling to source all they need.