Centrepoint fears that refugees will be denied access to benefits and public services during the "probationary citizenship" phase, outlined in proposals for the new citizenship process.
The charity claims the measures aimed at ensuring migrants "earn" citizenship, goes against the 1951 United Nations Refugee Convention, which states that refugees must be provided the same "public relief and assistance as is accorded to their nationals".
Asmerom Woldegebriel, Centrepoint's refugee advisor, said: "The grant of long-term protection to refugees who have fled persecution cannot be something that refugees have to earn.
"By limiting access to public services, these proposals will limit their ability to access education and work, making it even harder to successfully integrate into British society."
More than a quarter of the homeless young people that Centrepoint supports are refugees.
The charity also fears that young refugees will not have the money to pay for the citizenship process with the test, application and ceremony totalling £1,000.
A Home Office spokeswoman said: "We have always made it clear people must earn their right to stay in the UK permanently by working hard, obeying the law and speaking English.We are currently consulting on how the points-based system may work and what attributes should attract points."
She added: "We have no intention of returning refugees who continue to need our protection nor do we have any intention of separating genuine families. That is why family members and refugees would achieve sufficient points to pass the test on the basis of their continuing family relationship or protection needs."
