Professor Stephen Powis, NHS England medical director, wrote to Superdrug after the pharmacy chain announced it would be offering Botox and dermal fillers on the high street.
Superdrug currently offers Botox for £99 and dermal fillers for between £125 and £349 for people aged 25 and over.
The procedures are available at its flagship store on The Strand in London as part of a trial before being potentially rolled out to other stores.
Following the intervention by Prof Powis, Superdrug has agreed to put in place extra safeguards to protect those suffering from anxiety about their body or another mental health condition.
Anyone wanting Botox or fillers will be screened for conditions such as body dysmorphic disorder using questionnaires developed by psychologists in the field.
Questions include how often somebody feels anxious about certain parts of their body, their level of distress and how often they look at the part of their body they hate.
Other questions focus on how often anxiety about their body interferes with day-to-day activities.
As part of the screening, if a nurse practitioner suspects somebody is suffering from poor mental health, they can urge customers to visit their GP or get help from the charity Mind.
A 14-day cooling off period would also be put in place.
Currently there is no statutory regulation for private cosmetic surgery.
Prof Powis said: “Pressures on young people’s mental health are greater than they ever have been, with families and the health service too often left to pick up the pieces.
“The lack of tough checks on cosmetic surgery means that the public is dependent on businesses taking voluntary steps to get their house in order, leaving people avoidably exposed to dangerous practices.
“Businesses that take action to deal with people responsibly, work to prevent harm and set themselves a high bar for their practices should make others follow suit.”
In a statement, Superdrug said: “We remain fully committed to including recommended protections for mental health.
“We met with the NHS to ensure we have the highest safety standards and quality of patient care.
“We’ve always assessed a patient’s mental health as part of our Skin Renew consultation process.
“This assessment is woven through the consultation by our trained and qualified aesthetic nurse practitioners, whose experience and qualifications far exceed current standards.
“Our consultations last an hour to allow our nurse practitioners time to undertake a full and extensive consultation.
“This enables us to ensure we understand our patients’ reasons for wanting aesthetic treatments.
“It also flags to our team any risks or concerns related to a patient’s mental health.”
Body dysmorphic disorder is thought to affect around one in 50 people.
Kitty Wallace, trustee for the Body Dysmorphic Disorder Foundation, said: “Studies show that fewer than 10% of patients with BDD are satisfied with the results of cosmetic procedures.
“It is important that these measures are in place to protect such individuals from potentially damaging and unnecessary procedures.
“Although their anxiety might reduce temporarily, they will often find themselves fixating on another part of their body that they want to change.
“We commend that Superdrug will be screening for the disorder and referring people who are positive to their GP and Mind.”