The Home Office has been given less than a month to respond to a damning five-page letter from the race watchdog on the issue.
Changes made in November 2006 required skilled migrants to meet more stringent criteria before being allowed to remain in the UK or take up jobs. Campaigners have maintained that up to 40,000 migrants could be forced out of the country.
Now CRE director of policy Nick Johnson has written to Lin Homer, director-general of the Border and Immigration Agency, expressing his concerns over the way the system was changed.
"We are of the clear belief that the race equality impact assessment (REIA) of the changes to the HSMP does not fully comply with the requirements of the Race Equality Duty," Johnson wrote.
The duty was introduced in the wake of the inquiry into the murder of Stephen Lawrence, and gives public bodies a duty to promote racial equality.
The CRE is concerned that the impact assessment was not published until after the HSMP changes came into effect. There was also insufficient evidence of the existing criteria being analysed, said the CRE, and a failure to address the potential adverse impact of the changes.
The CRE has given the Home Office until 5 July to "address the substantive concerns identified and incorporate these into the policy".
Amit Kapadia, director of campaign group the HSMP Forum, said the CRE's findings showed that the government's changes were "ill intended".
A Home Office spokesman said: "We will respond fully to the letter when we have gi