Nationwide industrial action by some tugboat engineers is continuing today with ports in New South Wales and Western Australia affected.

The strikes are part of an ongoing dispute with the international towage company Svitzer.

Martin Byrne from the Australian Institute of Marine and Power Engineers said the stoppage would be in place for two days, ending at midnight on Tuesday.

"So Svitzer is the major operator and certainly it is the only operator of large commercial tugs in Sydney, Botany, Fremantle and Kwinana," Mr Byrne said.

Mr Byrne said four more ports would be affected tomorrow.

Last week, ports in Newcastle, Sydney, Geelong, Brisbane and Melbourne were affected.

The industrial action comes after unsuccessful negotiations for a new enterprise agreement, with engineers rejecting attempts by Svitzer to bring them under the same agreement as deckhands and tugboat skippers.

Mr Byrne said almost all of the commercial shipping in the four ports targeted today would be affected, with exemptions for cruise ships, military and those ships affected with safety issues.

Svitzer's application to terminate industrial campaign rejected

The Fair Work Commission last week rejected Svitzer's application to terminate the union's industrial campaign.

A spokeswoman for the commission said the application to terminate the unprotected industrial action was rejected, however no order was made on the protected action, saying the Commission could revisit it if there was a change regarding health or economic matters.

"Subsection 424(1) of the Act provides that the Fair Work Commission must make an order to suspend or terminate protected industrial action that is being engaged in, or is threatened, impending or probable, if it is satisfied that the protected industrial action has threatened, is threatening or would threaten to endanger the life, the personal safety or health, or the welfare, of the population or part of it, or to cause significant damage to the Australian economy or an important part of it."

In a statement issued late last week, Svitzer said it was disappointed with the ongoing action.

"While Svitzer appreciates that under the Fair Work Act, employees have the right to withdraw their labour in pursuit of their industrial goals, we are nonetheless extremely disappointed with the outcome," the statement read.

"For an island nation like Australia, which relies on the maritime industry to move 99 per cent of its industrial trade, the stoppages will damage the Australian economy and put jobs at risk."

NSW Ports said the industrial action would have a big impact on trade and cost to operators.

Chief executive Marika Calfas said 13 ships would be affected at Port Botany over the next two days.

"The rule of thumb is that for every 24 hours of delay, it takes about four days to catch up," Ms Calfas said.

"That is because Port Botany is also a busy port so we don't have gaps between days where there is nothing happening. We have always got ships coming in, ships going out."

She said it cost in excess of $50,000 per day for each ship delayed.

Ms Calfas said disruptions to port operations at Port Botany affected everyone.

"The disruptions have wide-ranging implications across all parts of the port's supply chain on the waterside and also on the landside. Disruptions to efficient port operations result in added costs to businesses and consumers," she said.

"Not just in Sydney and NSW but across Australia and they also have the potential to impact on Australia's reputation as a place to do business."

Ms Calfas said some of the ships delayed were carrying bulk liquids such as liquid petroleum gas.

Svitzer said its entire workforce would have an opportunity to vote on the proposed new Enterprise Agreement (EA). It said the EA has the in-principle support of the other two maritime unions - the Maritime Union of Australia and the Australian Maritime Officers Union.

Mr Byrne said his union would be recommending its members vote against the proposed EA this week.