''We're really pleased that the penalties in the legislation were changed to make it possible.''
It was unlikely the geckos could be released to the wild, Mr Agnew said.
''Potentially they could have diseases.
''They might need to be held in a secure facility longer term.''
It was not known what other animals they had contact with while being held by the poacher.
In March 2013, New Zealand led the effort to improve protection of jewelled geckos under the Convention on International Trade in Endangered Species of Wild Fauna and Flora. The change gave international authorities more power to investigate suspected poaching.
Eco Gecko consultant Carey Knox, of Dunedin, identified one of the geckos as being from the Otago Peninsula by using a photograph he took several years before they were seized.
Jewelled geckos can be identified as individuals by unique patterns on their backs. Mr Knox said he was glad to play a role in their return.
''I hope it sends a message that these animals belong in New Zealand, preferably in the wild.
''However, since these two geckos cannot be returned to the wild, I hope that they can play an important educational role in captivity.''
Associate Conservation Minister Nicky Wagner said the return of the geckos sent a message that wildlife crime would not be tolerated.
''This is the first time that poached, live New Zealand wildlife has been repatriated from overseas.''
All species of green gecko, including jewelled, were in decline because of both predators and poaching, she said.
''For many New Zealanders, geckos are considered a taonga or treasure so we are delighted that the hard work of New Zealand and German authorities has resulted in their return,'' Ms Wagner said.
