The pharmaceutical company was slated after telling the British Pregnancy Advisory Service (BPAS) it was avoiding "incentivising inappropriate use".
The BPAS has lobbied Boots to reduce the cost of the pill to make it more accessible for women having difficulty getting the drug quickly on the NHS.
Competitors had halved their price of the contraception pill with the branded drug Levonelle costing £13.50 at Tesco and a generic version costing £13.49 in Superdrug.
A spokesman for Boots was quoted as saying: "Pharmacy and care for customers are at the heart of everything we do and as such we are truly sorry that our poor choice of words in describing our position on emergency hormonal contraception (EHC) has caused offence and misunderstanding, and we sincerely apologise."
Claire Murphy from BPAS welcomed this news and said that it was a result of men and women of this country making "their voices heard in response to the position Boots originally took."
However, in a previous interview on Premier, a spokeswoman for the Society for the Protection of Unborn Children (SPUC), Alethea Williams, had agreed with Boots' previous stance, stating: "So the fact that Boots are not giving into pressure to make it more readily available - while they are willing to sell it which is not wonderful, at least they're showing some sort of responsibility on this."
Boots had formerly defended its pricing plan for the pill, saying it was often contacted by individuals who criticise the company for providing the service.