The Catholic charity, which provides spiritual support to seafarers, announced the redundancies after a strategic review.
The charity, which began life as a Jesuit-led organisation in Glasgow in 1899, employs about 30 staff.
Captain Paul Quinn, national director of the charity, said the job cuts would bring the charity back to a stable financial situation.
"This painful process must be endured in order to continue our vital work in the ports," he said. "We do not take these decisions lightly, but we have to consider our mission."
The organisation had previously warned that jobs were at risk as a result of falling donations through churches (Third Sector Online, 29 July).