Since the ruling police have switched off hidden cameras in 13 active operations, affecting 45 suspected offenders.
The Government is trying to fast-track an interim measure to give agencies the right to turn their cameras back on.
Yesterday the office of Attorney-General Chris Finlayson confirmed the SIS was among the affected agencies.
This raises questions of how well the SIS can do its work without video spying.
Global security expert Paul Buchanan said the SIS commonly used covert video surveillance, including to keep a close eye on domestic groups during the Rugby World Cup.
"If you were a domestic group with grievances of an environmental or sovereignty type, you could cause quite a splash," he said. "They'd be remiss if they had not [used video to monitor such groups] to see if there were potential threats."
Dr Buchanan said the SIS also commonly used hidden cameras for counter-espionage.
"We think of espionage as being political and military, but a major component of Government espionage - be it from the US, France, Germany, Australia or China - is to acquire proprietary information of an economic sort.
"The SIS has regularly reported that it believes New Zealand to be the target of such espionage ... New Zealand has a discreet but thriving [private] weapons component industry."
When asked how vulnerable the decision left New Zealand, Dr Buchanan said it was a "gap in the armour".
"But they were doing quite well (including bugging devices) before they had video technologies and before they were able to do things on private property."
He questioned whether the SIS would stop filming, even though it was illegal in the eyes of the Supreme Court.
CANDID CAMERAS
Supreme Court: Use of covert video surveillance on private property is illegal.
Crown Law: Decision affects Government agencies including the SIS, which uses video tracking to monitor threats from spies from foreign governments and domestic dissident groups and events, including the Rugby World Cup.
Security expert: Says it leaves a gap in New Zealand's armour.