The attorney general has questioned whether there can be separate donor systems operating in the UK The assembly and UK governments remain at odds over whether an opt-out organ donor system in Wales would be legal.
It follows objections expressed as “fundamental concerns” by the attorney general about a separate system in Wales.
Health Minister Edwina Hart has told AMs that she had clear advice that the move was legal.
Welsh Secretary Cheryl Gillan has rejected criticism over how the issue is being handled.
The assembly government wants to bring in a soft opt-out system whereby people in Wales would need to indicate that they do not want their organs given for transplant when they die.
Supporters say it would help make more organs available for patients who need transplants.
But before the proposed system of presumed consent can be put in place, the UK parliament must agree the details of the new powers, as part of a legislative competence order (LCO).
However, as Ms Hart prepared to report on the progress of the LCO on Wednesday, she was given details of objections from the Attorney General Dominic Grieve – the UK government’s most senior law officer.
An assembly government source told BBC Wales the email containing the objections was sent from the Wales Office only 14 minutes before Mrs Hart was due to give her statement.
An absolute bombshell. We understand that the first minister was told on Monday in a meeting with the secretary of state that there could be some difficulties.
One AM said to me that this was a total lack of respect for the views of the elected members here in Cardiff Bay.
The clock is ticking – we are coming up to assembly elections.
I think this could well end up in the courts – it certainly is not going to go through in the smooth fashion some ministers in government in Cardiff Bay had been hoping.
Concerns included whether the LCO was outside the devolved areas, and the practicalities of having a different system in Wales for organ donation to that in England.
But Ms Hart said the assembly government’s view was that the order was lawful “and we would intend to proceed with it”.
One assembly member later told BBC Wales that they felt elected members in Wales had been shown a lack of respect for their views on the issue of organ donation.
But Mrs Gillan said in a statement the LCO was being handled “in exactly the same way” as all other legislative bids from the assembly government.
She said she had “worked closely” with assembly government ministers, including talks on Monday with the first minister, raising potential difficulties with the process.
“It is routine for the government to seek the view of the attorney general on all LCOs, and to obtain government agreement for LCOs to be submitted for pre-legislative scrutiny,” she said.
She said they had reached this stage against a “very tight timetable” and it was now going for detailed scrutiny.
Kidney Wales Foundation chairman Roy J Thomas said “sending emails late in the day on matters of such importance is a major concern”.
He added: “We see it as being very legal [in Wales], and indeed if Westminster or Whitehall chose to challenge that – we would also challenge their view.”
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