Tories, Lib Dems and some Labour MPs oppose the bill
Plans to extend the limit on detaining terror suspects without charge to 42 days could face an Equality and Human Rights Commission court challenge.
They say plans to increase the limit from 28 days could contravene the law.
Home Secretary Jacqui Smith says it is the commission's job "to challenge and scrutinise", but said Parliament should have its say before any court case.
She added that her plan was intended to safeguard the "most fundamental right" - not to be a victim of terrorism.
The Home Office said it had consulted to win as much consensus as possible.
Ministers have come up against strong opposition from Tories, Lib Dems and some Labour MPs over terror detentions.
The commission says the proposed law could contravene race equality legislation, as it is being established to deal with a particular religious and racial minority.
It told MPs in a briefing note: "If adopted, we may seek to use our legal powers to challenge the lawfulness of the provisions and establish clear legal principles on the use of pre-trial detention."
The watchdog says the provisions set out by the Home Office are unlikely to meet threshold tests of public interest, justification or fairness.