The Australian Council of Trade Unions says there is no evidence the deals will create jobs in Australia or improve wages.

Labor MPs decided at a special caucus meeting on Thursday morning to back the trio of deals but to seek further safeguards from the government on how they will be implemented.

ACTU president Michele O'Neil says the decision to side with the government abandon's Labor's national platform and its responsibility to stand up for fair trade deals and Australian jobs.

"They've made a mistake that will not be forgotten by Australian workers," she said.

And the Victorian branch of the Electrical Trades Union made the attack personal on leader Anthony Albanese.

"These deals are bad for Aussie jobs and let multinationals sue Australia if our laws hurt their profits. When is Albo going to stick up for Australian workers?" the union tweeted.

As well as unions, Labor was under pressure from churches and aid groups to block the bill due to concerns over provisions allowing foreign companies to sue the government.

Fears have also been raised the Indonesian deal will exploit workers.

Opposition trade spokeswoman Madeleine King has written to minister Simon Birmingham seeking a guarantee that local jobs will be protected, a review of clauses that would let companies sue the government if its law changes adversely affect them, new rules around working holidaymakers, the termination of old treaties, and an assurance that no treaty will force the privatisation of any services or public assets.

"Labor will fight to ensure that the implementation of the Indonesia, Hong Kong and Peru trade agreements fully achieves the goal of creating Australian jobs and opening opportunities for Australian exporters," she said in a statement.

Senator Birmingham welcomed Labor's intention to pass the legislation and said the government will go through its conditions.

Asked on Sky News whether jobs can be protected under a trade deal like this, the minister said: "We have an open economy, some businesses grow, some businesses fail."

"What I can say is the proven experience of the trade deals we've done under this government is Australian export volumes are growing, we have have been recording record trade surpluses," he said.

The government says the deals will lead to Australian grain growers being able to export 500,000 tonnes of feed grains into Indonesia, remove tariffs on goods exported to Hong Kong, guarantee market access for services suppliers, and improve conditions for two-way investment.

Australian dairy farmers would also have new access to Peru with no tariffs on up to 7000 tonnes of products.

Australian Associated Press