Construction has been on hold since a single great crested newt was spotted two months ago.
The delays are estimated to have cost the force about £150,000 but Natural England said it hoped to allow work to continue soon.
Durham Police said it was working with the conservation body to resolve the issue “as quickly as possible”.
The great crested newt is protected under the Wildlife and Countryside Act 1981 and permission for their removal must be granted by Natural England.
Planning permission was granted for the new headquarters in June and work was scheduled to start in December.
A Kier spokeswoman said: “We have come across situations like this on a number of jobs.
“It’s something we deal with as part of the project management process and we always work closely with our clients and the appropriate agencies to ensure that we abide by the relevant legislation, while keeping the project running as smoothly as possible.”
Assistant Chief Officer Gary Ridley said: “We are sitting here with a scheme, ready to go and are waiting for a licence to be granted so we can mobilise the contractor to start the work.”
A Natural England spokesman said: “We are treating this case as the highest priority.
“We are working flat-out to process the licence application and hope to complete this in the next few days.”
Ridley added: “Once the licence has been granted the building work will most probably start 6-7 weeks after that. Hopefully the new HQ will still be on track to open in the summer of 2014.”