Corrections Minister Judith Collins says some parts of Christchurch prison buildings have not withstood the earthquake.
All of the 135 women at Christchurch Women's Prison have been moved to Auckland, and about half of the 800 inmates at Christchurch Men's Prison have been moved to North Island prisons.
Ms Collins says that if the prison buildings are found to be unsafe, they will be repaired or demolished and replaced.
She says she hopes the smaller muster will ease the pressure on Canterbury prison staff. The remaining inmates at the men's prison are lower-security prisoners, she says.