Tescos is participating, along with other supermarkets and pharmacies, in a government-backed pilot scheme aimed at reducing teenage pregnancies.
However, it acknowledged today that local residents had expressed their concern about underage girls having easy access to emergency contraception without the knowledge or consent of parents.
From Thursday, pharmacists in Tesco stores will ask for proof of age from teenage girls.
A spokesman said: "The changes we have made reflect how we listen to customers and react to their concerns."
Powerful drug
Emergency contraception, commonly called the "morning after pill", can in fact be taken up to 72 hours after sex, and works by blocking pregnancy even if the egg has been fertilised.
It contains hormones at much higher levels than those in the current contraceptive pill.
It is currently available only on prescription, but the government is testing whether wider access would reduce the rate of teenage pregnancy.
Pro-life groups have welcomed the decision to place more stringent controls on the availability of the pills.
They claim that there is no evidence that emergency contraception reduces teenage pregnancy.
A spokesman for Life said: "Tesco as standard-bearer of the retail food industry is setting an example of real concern for the health of young girls in the UK."
Figures from the pilot scheme suggest that fewer than 1,000 consultations about emergency contraception have been carried out at Tesco - and that only 7% of these involved people aged under 16.