A toxic cocktail of fuel and fertiliser has been lost from a cargo ship off southeast Queensland, raising fears of ecological damage.

Amid fierce seas whipped up by Cyclone Hamish, 31 containers carrying 620 tonnes of ammonium nitrate toppled into the sea off Moreton Island yesterday.

Up to 30 tonnes of oil also leaked from the ship creating a slick that covers an estimated 5.5km by 500m, drifting in a northwesterly direction.

The lost containers damaged the hull of the 180m Pacific Adventurer, causing the oil to spill.

Maritime Safety Queensland (MSQ) said the vessel and its 15 crew, who left Newcastle on Tuesday bound for Brisbane, had anchored in calmer water in Moreton Bay as a precaution and to carry out a damage assessment.

MSQ general manager John Watkinson said about one tonne of ammonium nitrate was covering the ship's deck but the chances of an explosion were low.

"The cargo is rather benign. It takes a significant mixing with certain other contaminants, which are not on the ship, or a pretty big ignition source and neither one are present."

Emergency services crews have assessed the ship as a precaution ahead of its expected arrival in Brisbane on Thursday morning.