More than nine in 10 domestic seafarers will lose their jobs if the Abbott government's plan to relax shipping regulations passes Parliament, research suggests.

Less than 100 seafarers would remain in employment out of a current workforce of 1177, according to a report written by the Australia Institute, based on government documents supporting its Shipping Legislation Amendment Bill.

Opponents to the shipping industry changes say they will cost jobs. Credit:Jessica Shapiro

The dire forecast comes as a major Bass Strait freight company, SeaRoad, warned it will reconsider a $100 million investment in two new cargo vessels if the government pushes ahead and dumps rules that force foreign vessels to pay their crew Australian wages while working domestic routes.

Stakeholders, including shipping industry representatives, the ACTU and three Senate crossbenchers, John Madigan, Ricky Muir and Jacqui Lambie, will meet in Melbourne on Friday to discuss the threat to jobs and national fuel security.