The order signed to suppress the involvement of the GCSB in the Kim Dotcom case was the only one of its kind made in the last decade.
The spy agency has stated that the certificate signed by Finance Minister Bill English as Acting Prime Minister was the only one found in "a thorough search of our files".
Mr English was asked by the GCSB to sign the "ministerial certificate" while Prime Minister John Key was overseas in August. The certificate said knowledge of the GCSB's involvement in the Dotcom investigation would damage its ability to detect or prevent serious crime.
The fact it was the only ministerial warrant in 10 years was discovered by the Green Party under the Official Information Act. Its rarity has led Green Party co-leader Russel Norman to question how Mr Key stayed ignorant of its existence until a month after it was signed.
Mr Key was only told after it emerged the GCSB's spying on the internet tycoon was illegal - a discovery which ruined the GCSB's bid for secrecy.