A free trade deal between Australia and Indonesia is being signed in Jakarta.

Trade minister Scott Birmingham and his Indonesian counterpart Enggartiasto Lukita say the deal will open markets for agriculture and education.

After eight years of negotiations, the agreement will see 99 per cent of Australian goods exports by value enter Indonesia duty free or under significantly improved preferential arrangements by 2020.

Indonesia has guaranteed automatic import permits for live cattle, frozen beef, sheep meat, feed grains, rolled steel coil, carrots and potatoes.

However, concerns have been raised about the deal’s labour market testing rules and investor-state dispute settlement (ISDS) clauses.  

ISDS clauses allow Indonesian investors to take legal action against Australia if they believe the treaty has been breached.

The Australian Council of Trade Unions (ACTU) calls it a “dodgy deal” that favours unlimited temporary visa holders.

The manufacturing workers' union says no one has provided substantive evidence that the deal will benefit Australian workers.

Labor is not standing in the way, with leader Bill Shorten saying “we're very positive from what we've seen so far”.

Reports say the Australian service industries set to benefit include mining, tourism, telecommunications and transport.

The education sector should be a winner, with universities granted improved access to Indonesia, which is looking to expand its higher education sector.