The new Qualifications and Curriculum Development Agency (QCDA) could face having its powers dramatically weakened if the latest Education Bill is to become law.
Legal recognition of the QCDA, along with Ofqual, is dependent on the Apprenticeships, Skills, Children and Learning Bill, which is currently bogged down in the House of Lords.
There are fears that time will run out before the legislation can be debated in its entirety ahead of it being given Royal Assent in November.
There are even concerns that the Bill, which also contains new powers giving teachers the right to search and restrain pupils, could fail to become statute altogether.
The House of Lords has only reached clause 47 of 250 with 200 amendments to be debated and there are only four committee meetings remaining to debate the Bill when the House returns from recess on October 12.
It is understood both the Liberal Democrat and Conservative peers are refusing to take part in all-night sittings to debate it and are demanding the Government hold back pieces of legislation for an alternative Bill or drop parts of it altogether.
The Lib Dems have written to the Government calling for compromises to be made in regards to the powers held by the QCDA, as well as powers granting the Secretary of State to direct which books should be read in the curriculum.
David Laws, Lib Dem education spokesman, described the scrutiny of the Bill in the House of Commons as a "disgrace" after MPs were forced into a "record breaking" all-night sitting to debate the remainder of the legislation.
Mr Laws said: "It is now clear that there is too little time for the Bill to receive proper scrutiny in the House of Lords. What would make sense would be for the Government to jettison some major parts of the Bill in order to allow time to focus on the key elements."
He added: "Some parts of this Bill could be brought back with the Government's next piece of legislation later this year and other ill-conceived parts should never see the light of day again."
Baroness Garden of Frognal, Lib Dem peer, told The TES that the Government had not been "hugely receptive" to their requests to drop or defer parts of the Bill and said there were "real concerns" that it would not be ready in time to be given Royal Assent.
The Conservatives plan to call for teachers' search powers to be increased and have raised issues in regards to the Young People's Learning Agency (YPLA), which will take over the running of the academies programme.
Despite these concerns, and in spite of the ASCL Bill yet to come into effect, Ed Balls, Schools Secretary, has already named civil servant Peter Lauener as the first chief executive of the YPLA.
The Department for Children, Schools and Families said it expects the legislation to be debated in time for the Queen's Speech in its entirety.
A DCSF spokesman said: "The Bill is currently being debated in the House of Lords and the expectation remains that it will receive Royal Assent in this Parliamentary session. There are no plans for any part of the Bill to be dropped."