US immigration authorities have held a Congolese asylum seeker and her seven-year-old daughter in separate detention centres for months, a new lawsuit alleges, stoking fears Donald Trump's administration plans to keep families apart in a bid to stem asylum requests.

In a claim filed on Monday in a US District Court in California, the American Civil Liberties Union (ACLU) said the mother and daughter have been detained since they arrived and filed for asylum in San Diego in November of last year.

Known only as "Ms L" in the court filing, the woman fled violence in her native Democratic Republic of Congo, which has been wracked by political instability, armed clashes, and an increasing humanitarian crisis.

While the mother is being detained in the San Diego area, her child is held more than 3,000km away in Chicago, ACLU said.

"The Trump administration is using this little girl and her mother as pawns in its draconian public policy experiment," said Lee Gelernt, deputy director of ACLU's Immigrants' Rights Project, in a statement.

The lawsuit accuses US Immigration and Customs Enforcement and the Department of Homeland Security, among others, of violating the plaintiffs' right to due process and violating federal asylum laws.

"Not only is it horrific to rip this child from her mother, there is no legal justification for it," Gelernt said.

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News of the family's months-long separation comes only two months after US media reported the Trump administration was considering a plan to keep parents apart from their children when they are caught entering the US without visas.

The plan is intended to discourage undocumented migrants from crossing the border into the US, the New York Times reported in December.

Trump campaigned on a promise to build a wall on the US' southern border with Mexico and crack down on undocumented immigration.

At least 200 US human rights groups recently condemned the forced separation policy, saying it would have "significant and long-lasting consequences for the safety, health, development, and well-being of children".

"Family unity is a foundational principle of child welfare law," MaryLee Allen of the Children's Defense Fund said in a letter to US Department of Homeland Security Secretary Kirstjen Nielsen in January.

"In order to grow and develop, children need to remain in the care of their parents where they are loved, nurtured and feel safe... The proposed changes to your agency's policies would eviscerate that principle."