The urgent meeting between London Underground and the Health and Safety Executive was called by the Deputy Prime Minister John Prescott.
He said the part-privatisation would not go ahead if there were safety fears due to the break-up of London Underground into separate organisations and claimed opponents of the partial sell-off wanted to "ride on safety".
But the Mayor of London, Ken Livingstone, said the issues raised by the railway inspectorate of the HSE could be serious enough to convince the government to undertake a major U-turn and drop its plans altogether.
The meeting follows the BBC's Newsnight programme's discovery of a copy of a letter sent by the HSE's principal inspector of railways to the manager of strategy at London Underground, Dr Mike Maynard.
The letter warned safety could be jeopardised by organisational changes put into place to prepare for the public-private partnership next year.
It also said there were "safety issues with potentially serious consequences".
Mr Livingstone said: "John Prescott is not going to push through a scheme if the inspectorate of railways is saying there are safety implications here - it would be political suicide."
System 'not working'
On preparations for part-privatisation, the contracts for which are due to be signed in the next few weeks, he said: "This system isn't working - this isn't like they are testing it out, this is the system they are about to sign contracts on.
"They have been running a shadow operation as it would be under privatisation and it is that operation that is not working."
Underlining what he said was the gravity of the situation, the mayor said: "The health and safety letter says 'we wrote to you last November with these 11 serious issues and nine are still outstanding'."
In a statement to Newsnight, the HSE said the letter was written to inform London Underground of concerns about the "implementation of management changes".
London Underground said: "The safety of our customers and staff was our overriding priority before shadow-running began, continues to be our overriding priority now and will remain so in the future."
Safety assured
Mr Prescott said he been assured by the chairmen of the HSE and London Underground that the safety case for the operation of the Tube had not been breached.
"This letter clearly reflects the frustration of the safety inspector regarding his relationship with his opposite number at London Underground," he said.
"In view of that I have asked LU and the HSE to meet to sort this out and give me a full report."
Mr Livingstone, who fought his mayoral campaign on a policy of raising Tube funding through bonds and a combination of fares and government grant, has threatened to use the courts to halt the sell-off.
His concerns over the plans to part-privatise the London Underground received some support in July from a cross-party group of MPs.
The Commons transport select committee told the government it must not lead to passengers "being subjected to intolerable overcrowding and delays".
The mayor will become responsible for the Tube early next year.