The Catholic charity, which provides spiritual support for sailors and has an annual income of more than £1m, said that its annual Sea Sunday appeal, which provides much of its funding, had been hit by falling church attendances.
It has spent much of its reserves building, in partnership with others, Seafarers Centres and establishing paid chaplaincy posts and volunteer ship visitors.
Captain Paul Quinn, the charity's new national director, has said he will carry out a strategic review of the charity's operations.
The charity is considering losing three chaplains - one each in England, Scotland and Wales - and is also reviewing training procedures and the value of its national conference.
"The changing face of the shipping industry means ports that were once busy are now no longer so, or the type of ships they serve no longer need our services," a charity spokeswoman said.
Funding shortfall means staff cuts at seafarers charity
Seafarers charity Apostleship of the Sea is preparing to lay staff off in response to a £300,000-a-year funding shortfall.