The High Court decided on Wednesday to allow the Society for the Protection of the Unborn Child to bring a judicial review of the decision to make the medication more easily available to over-16-year-olds.
Previously it was only available on prescription from a doctor.
The High Court decision does not mean a reversal of the current policy - but simply allows the case to be heard in full.
The Society for the Protection of the Unborn Child (SPUC) claims that the "morning-after pill", which can be taken up to 72 hours after intercourse, is in fact a method of early abortion, and, as such, should be subject to abortion legislation.
Pharmacists who supply the Levonelle-2 pills, says SPUC, could be committing a criminal offence.
John Smeaton, SPUC's national director, said he was "absolutely delighted" with the decision.
He said: "This is a major public policy issue affecting the health of women in this country and in particular young women - which coincidentally is a case of the government seeking to circumvent the Abortion Act.
"Here we have pharmacists having the burden imposed on them of providing abortion by the morning-after pill in a totally unsupervised way, and no-one knows the impact of this drug on women."
An attempt has already been made in the House of Lords to prevent the medication being sold over-the-counter.
Conservative Baroness Young had argued that pharmacists were too busy to offer enough medical advice to women buying the pill.
She said she was also concerned that under-16s were buying the pill.
However, this attempt was defeated by peers.
A spokesman for the Family Planning Association said that she found the legal challenge "extraordinary", particularly as the Attorney General had, in the 1980s, already ruled that emergency contraception did not constitute a form of abortion.
She added: "The Family Planning Association wholeheartedly supports its use.
"It seems to be just an attack on women's health, and most misguided."