Right to Life (RTL) sought several declarations, including one that the committee had no power to issue FPA a licence limited to the first nine weeks of pregnancy.
And RTL said the law did not allow licences limited to medical abortions only.
When first granting the licence, the committee noted the nearest abortion clinic was at Thames Hospital, a clinic only performing surgical abortions.
The High Court heard licences were automatically renewed unless a clinic was found to have not complied with the Contraception, Sterilisation, and Abortion (CSA) Act.
In a judgement released today, Justice Joseph Williams said according to the CSA Act, only parties dissatisfied with the refusal to grant a licence could appeal to the High Court.
"No party aggrieved by the grant of a licence (such as RTL) has any appeal right."
Justice Williams said Right to Life could have brought proceedings in a judicial review.
The committee's barrister Wendy Aldred said RTL had no direct or personal interest in the case.
But Justice Williams said the High Court previously found "credible purpose-based organisations" did have standing in respect of "instruments affecting their purpose".
He found RTL had standing, and the case proceeded.Right to Life's barrister Peter Mckenzie QC said some of FPA's own literature highlighted risks associated with early medical abortion.
The court heard the clinic had arrangements to transfer patients to Tauranga Hospital in case of emergencies.
Justice Williams said there was no evidence the facilities and arrangements related to the clinic's procedures were unsafe.
Ultimately the judge declared that the limited licence renewals for this year and last were unlawful, in that they used the phrase "within the first nine weeks (up to and including 63 days of pregnancy)".
But Justice Williams said the correct wording for limited licences had to be "only during the first 12 weeks of pregnancy".
He did not void the licence, saying the unlawful wording could be changed and immediately substituted.
Costs were reserved.