The Immigrant Council of Ireland said the Government should immediately outline what procedures are in place across all public services to prevent racial profiling.
It said the two high-profile cases involving children from the Roma community have raised questions over whether minorities are being subjected to excessive attention from gardai.
Denise Charlton, chief executive of the Immigrant Council, said: "Ireland has already been warned by a Council of Europe report in February about the need to prevent racial profiling, and the events of the past week have done little to reassure migrants that this has taken place.
"The placing of two children from the Roma community into care comes just one week after the Government announced that people from abroad would account for a disproportionate 50% of social welfare checks as part of a new crackdown on fraud.
"Any targeting of members of an individual community for such scrutiny, on the basis of unfounded perceptions that they are more likely than others to break the law, is wrong."
Ms Charlton said robust anti-racism policies and procedures are key to ensure fair access to and delivery of our public services.
"It is time for the Government to outline what procedures are in place to reassure people, both Irish and migrant, that no one need fear being targeted because of their background, belief or colour of their skin," she added.
Children's Minister Frances Fitzgerald said that, while she could not comment on individual cases of children being taken into state care, she insisted the child's best interest is always paramount.
"Child protection is at the centre of any decisions that are taken, where gardai or social workers act in cases where children are taken into care," Ms Fitzgerald said.
"It's always about child protection and the best interest of the child."
The minister said there are currently 6,000 children in state care in Ireland - a number that has been rising.
"Children coming into care unfortunately is a common occurrence in Ireland at present, but compared to other countries we do not take many children into care," she said.
She encouraged members of the public to remain vigilant and contact the authorities if they have suspicions about the welfare of a child.
"As Minister for Children, I would be encouraging people to report if they are concerned about children," she said.
"We are going to put Children First (national guidance for the protection and welfare of children) on a statutory basis to make sure if there are real concerns about child abuse of child protection that they are reported. It is extremely important that the public are vigilant."
Ms Fitzgerald added that there had been "shocking figures" highlighting the level of unaccompanied children arriving in Ireland over the last 10 years.
She said that, while these numbers are now "going down dramatically", the state has a series of supports in place for trafficked children.
"It's a reflection of a worldwide problem," she said.
"That's a very serious issue worldwide, the trafficking of women and children, and Ireland is not immune to that.
"Obviously every action has to be taken to investigate all the circumstances where such an incident occurs."