Some operations got repeat warrants. In the case of interception warrants, while there were seven operations, some required new warrants to be issued and a total of 11 warrants had been in force over the period, not the seven originally stated.
Five new interception warrants - used for tapping phones for example - had been issued, not the four as originally stated.
The biggest error was on the number of access authorisations - for access to computers for example - with 26 having been in force over the period, not the 14 originally stated.
And 11 new access authorisations were issues, not nine as originally stated.
Mr Key's spokeswoman issues a statement saying: "The Prime Minister is unhappy that the error has been made and has received a letter expressing regret from GCSB Director Ian Fletcher. The Prime Minister has been advised that the error stems from GCSB mistakenly counting the number of operations rather than the number of warrants on issue. There was no attempt to deliberately mislead. Further, he has been advised by the Director that steps have been taken to ensure the error cannot happen again."
The Rebecca Kitteridge review of the GCSB was ordered after it admitted its spying on internet businessman Kim Dotcom was unlawful because he was a New Zealand resident - and it found the number of unlawful was over 80.
Labour leader David Cunliffe said the "latest embarrassing blunder" proved why a review into all of New Zealand's spy agencies should be held, which is what a Labour Government would order.
It was "mind-boggling" the GCSB couldn't get the number of warrants it had issued correct in its annual report.
"The bureau has a lot of work to do to restore confidence."
The latest blunder would do nothing to reassure New Zealanders the spy agencies were competent.
Greens co-leader Russel Norman said it was "another serious mistake by the GCSB" and raised questions about its ability to do its job.
The mistake was not a small one.
"It cuts to the heart of their accountability to the Government and the New Zealand public."
"The number of interception warrants and access authorisations is force and new ones issued over a year is bread and butter stuff. They should not be getting this sort of thing wrong."