Labor has accused Immigration Minister Scott Morrison of trying to silence his critics by cutting more than half a million dollars from refugee advocates.

The Refugee Council of Australia has been told it will not get the funding, totalling $560,000 over four years, allocated to it in the federal budget just weeks ago.

Council chief executive Paul Power says Mr Morrison made the decision.

“This decision is petty and vindictive and is symbolic of the minister’s very poor relationship with the non-government sector,” Mr Power said in a statement.

A spokeswoman for Mr Morrison said the government had returned to the Howard-era funding model.

“This decision has been taken in light of the tight fiscal environment and budgetary constraints,” she said.

The Howard government withdrew the council’s core funding in 2002. It was restored when Labor won power in 2007.

The opposition said the decision proved Mr Morrison was only interested in chest-beating about border protection, with no regard for the wellbeing of people fleeing persecution.

“This is a government who will punish its critics,” Opposition Leader Bill Shorten told reporters in Melbourne.

“It’s not the right way in the Australian democracy.”

The refugee council, established in 1981, is a network of 185 organisations, 800 individual members and thousands of supporters.

Mr Power said its relationship with various governments had waxed and waned over the years but communication had never been poorer than now.

The $140,000 annual grant is almost a quarter of the council’s budget.

“It will hurt us but we have no intention of reducing our small staff team or allowing this cut to distract us from raising a voice for justice and compassion for refugees,” he said.

The Australian Greens said the funding cut was a nasty ideological attack, designed to shut down dissent.

“This spiteful cut is just the latest in a long line of attacks on groups who don’t always agree with the government,” Greens Senator Sarah Hanson-Young said.