The crew of an Australian-operated petrol tanker are refusing to leave their ship in a dispute they say goes to the issues of national fuel security and threats to the marine environment posed by unsafe foreign-flagged vessels increasingly operating in local waters.

The Tandara Spirit is anchored in Melbourne's Port Phillip Bay, where its crew of 18 has been staging a sit-in for the past 15 days since the owners of Shell's former Geelong refinery ordered them to sail to Singapore, where they would be made redundant.

The ship, one of just five Australian-crewed petrol tankers left, is to be handed back to its owners after Viva Energy, the company that bought Shell's Geelong refinery and 870 service stations, said it had no need for the Tandara Spirit, which has mainly been used to ship petrol to Adelaide.

But as the Australian crew began their protest and refused to sail, Viva Energy had already chartered an alternative Vietnamese-crewed tanker with a chequered safety record to transport fuel on the same Geelong-to-Adelaide route.

Inspectors from the International Transport Workers Federation, who boarded the Vietnamese tanker, the Vinalines Galaxy, on November 14, found its crew are paid about $2 an hour – or $20 a day.

According to maritime data provider Sea-web, the Vinalines Galaxy has been inspected three times by the Australian Maritime Safety Authority since December 2011 and has been hit with a total of 49 defect notices, including "pollution prevention", "fire safety" and "working and living conditions" breaches.

Since 2004, none of the five Australian-crewed petrol tankers has been detained by AMSA over a serious defect, according to the Maritime Union of Australia.

Australia now imports 91 per cent of its petrol and diesel – up from 60 per cent in 2000. NSW has no refineries left open and groups like the NRMA have flagged concern that the country has less than 12 days of diesel stock.

Maritime environment campaigners the Victorian National Parks Association said the risk of fuel spills was heightened by defective ships and that could prove catastrophic in Port Phillip Bay, which is a habitat for migratory birds from as far away as Siberia.

Since it bought Shell's "downstream business" in August for $3 billion, Viva Energy has applied to the federal Department of Infrastructure and Regional Development for 16 temporary licences to ship fuel between Australian ports.

In a statement, Viva Energy confirmed its intention to hand back the fuel tanker once its lease expires in January and said it "will not be replacing the vessel".

"As a result of agreeing new contracts which significantly increase ground fuel sales in Victoria, Viva Energy's requirement to export product from Victoria has considerably reduced. Consequently, Viva Energy no longer requires a dedicated coastal vessel to transport petroleum products within Australia," it said.

"Viva Energy applies for and uses temporary licences and this includes transporting specialty products to multiple ports [which the Tandara Spirit does not carry]."

But maritime experts point to Viva's own boast on its website that it supplies 25 per cent of Australia's petrol but its one Geelong refinery only produces 13.5 per cent, indicating that it has a massive transport task.

Fairfax Media has learnt that on Thursday, two foreign-flagged tankers – both twice the size of the Tandara Spirit – were loaded with fuel product at the Geelong refinery. They will be anchored in Port Phillip Bay to store the fuel for a month, according to maritime sources.

Viva Energy was spun out of the $US300 billion Swiss-based oil trading company Vitol, which has been at the centre of a number of international scandals, including a tax dodging investigation by authorities in Britain last year.

The company controversially supplied fuel to the regime of Serbian despot Slobodan Milosevic. It pleaded guilty to grand larceny in a New York court for circumventing sanctions against Iraqi dictator Saddam Hussein and bought and sold Iranian oil during sanctions against Tehran in 2012, according to an investigation by Reuters.

Matt Ruchel, executive director of the Victorian National Parks Association, which has campaigned on marine safety said Port Phillip Bay in particular was sensitive to shipping spills due to its largely enclosed nature.

"The risk of some kind of damaging oil or fuel spill from ships that are not up to scratch is much higher," he said.

A crew member of the Tandara Spirit, Kevin Millar, said it was obvious Viva Energy would continue to ship fuel on the same routes after it chartered the Vinalines Galaxy.

"Australia is using and importing more fuel and it needs to move around the coast. Why not get Australian crews to do it? It's a disgrace that Vitol or Viva want to replace us with workers earning $20 a day," he said.

The operator of the Tandara Spirit, Teekay Australia, and the crew, represented by the MUA, are due at the Federal Court next week after the Fair Work Commission earlier ordered the two parties to negotiate.

Fair Work was earlier receptive to complaints that Viva Energy had not adequately consulted under the terms of its enterprise bargaining agreement before ordering Teekay to order the crew to sail to Singapore.