The migrants are being taken to a port area where there will be tent sites for around 1,700 people with beds and shower facilities, according to the authorities.
The movement began early on Friday and police are reported to have had difficulty controlling the crowds at times.
Ceuta was overrun at the end of July when more than 70,000 migrants crossed the border from Morocco in a chaotic manner.
The vast majority have returned, but exactly how many remain is unclear: According to authorities in the exclave, there are around 13,000, but the Spanish central government says the number of remaining migrants is lower.
The crisis has had major political consequences, including Italy introducing border controls against Spain.
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