Security by design, or alternately secure by design, means that the software has been designed from the ground up to be secure. In this case, security is considered as a main feature.
Some of the techniques in this approach include:
The principle of least privilege, where each part of the system has only the privileges that are needed for its function. That way even if an attacker gains access to that part, they have only limited access to the whole system.
Automated theorem proving to prove the correctness of crucial software subsystems.
Code reviews and unit testing, approaches to make modules more secure where formal correctness proofs are not possible.
Defense in depth, where the design is such that more than one subsystem needs to be violated to compromise the integrity of the system and the information it holds.
Default secure settings, and design to "fail secure" rather than "fail insecure" (see fail-safe for the equivalent in safety engineering). Ideally, a secure system should require a deliberate, conscious, knowledgeable and free decision on the part of legitimate authorities in order to make it insecure.
Audit trails tracking system activity, so that when a security breach occurs, the mechanism and extent of the breach can be determined. Storing audit trails remotely, where they can only be appended to, can keep intruders from covering their tracks.
Full disclosure of all vulnerabilities, to ensure that the "window of vulnerability" is kept as short as possible when bugs are discovered.