Twenty-one boxes containing 7,000 seed samples from 36 African nations were sent by the Nigeria-based International Institute of Tropical Agriculture.
The final leg of the journey will take the seeds to the remote Arctic Island.
The vault is intended to act as insurance so that food production can be restarted anywhere on Earth after a regional or global catastrophe.
Built deep inside a mountain, the structure will eventually house a vast collection of seeds; safeguarding world crops against possible future disasters including nuclear wars and dangerous climate change.
The temperature inside the Svalbard Global Seed Vault will drop to -18C (0F) in order to preserve the seeds.
The Norwegian government is paying the $9m (£4.5m) construction costs of the vault, which will have enough space to house 4.5 million seed samples.