Indonesia has threatened to ban Australian beef imports amid concerns some of the meat doesn't meet Islamic halal standards.

A large amount of Australian beef is being held at Jakarta's main port because the country's Islamic Ulema Council, or MUI, has declared it no longer recognises several of Australia's halal certifying bodies.

Indonesia, which imports an estimated 70,000 tonnes of beef from Australia and New Zealand every year, requires all beef imports to be certified halal.

That means the meat has been taken from cattle slaughtered in a manner deemed suitable for consumption by Muslims. But it's up to the MUI, Indonesia's top Islamic body, to decide which overseas institutions can certify the meat.

Indonesia this week temporarily banned beef imports from New Zealand after the MUI announced it no longer recognises any of that country's certifying bodies.

According to the state-owned news agency Antara, Agriculture Minister Anton Apriyantono said Australian certifying bodies had to meet new MUI standards or Australian beef would face a similar ban.

A spokesman for the Trade Minister Simon Crean said the government was concerned that Australian beef was being held up at Jakarta's Tanjung Priok port.

"Mr Crean is hopeful that Australian and Indonesian officials can work together to ensure that the free flow of trade in Australian beef is restored as soon as possible," the spokesman said.

Mr Crean will raise the issue with his Indonesian counterpart Mari Pangestu at a trade meeting in Bali at the weekend.

Halal Australia executive director Muhammad Khan said it was disappointing to see the beef held up. "There's a bit of a communication gap going on," he said. "If it's not allowed in, exporters should be told at the port of departure in Australia."

If the matter is not resolved, the meat already in Jakarta will either be re-exported or destroyed, Indonesia's agriculture department said.