A spokeswoman for the agency confirmed an order had been issued but said it was only to safeguard the land needed for its Olympic Park and that Stratford City was not in danger.
She said: 'We are absolutely committed to the regeneration of this area and the delivery of the Olympic Park and Stratford City.'
She admitted, however, that a compulsory purchase order covering the entire site of the Olympic Park had been unanimously agreed by the LDA board.
It would be issued 'imminently', she said, but added that this was what the LDA had always said it would do.
The agency had been negotiating with private consortium LCR because some land currently under LCR's control overlapped onto the Olympic Park site.
Negotiations reportedly broke down last week and a crisis meeting between Mayor Ken Livingstone, Deputy Prime Minister John Prescott and Culture Secretary Tessa Jowell was called yesterday to try and end the deadlock.
But the LDA board then met and decided unanimously that a compulsory purchase order should be put in place to cover all the land set aside for the Olympic Park.
A statement by London and Continental Railways declared it was 'shocked, amazed and deeply disappointed at the decision'.
It said: 'It is incomprehensible that the LDA should seek to effectively kill off the consented £4 billion, 13.5 million square feet Stratford City regeneration project, which LCR has spent a decade working on and which has been fully approved and endorses by Newham council, the Mayor and Government earlier this year.
'Up to now the planning process for Stratford City has progressed well and it is utterly perplexing that such a cornerstone of the Olympic legacy is placed in such severe jeopardy.'
The LDA spokeswoman maintained today that the CPO would not 'in any way stop individual negotiations with landowners'.
'These negotiations will continue, for small businesses and all land owners. This CPO is a safeguard only. We did this to ensure that everything is delivered for the Olympic Park. However, we do want to continue the private negotiations.'
Some 81 per cent of the land needed is already in public control and this is about acquiring the remaining 19 per cent, she said, although she added that the order would not need to be enforced if private deals went ahead instead.
She confirmed that London and Continental Railways were covered by the order because the Stratford City development lies right next to the Olympic Park development.
'They have land required as part of the Olympic Park and as with any landowner they are covered by the order,' she said.
But she claimed both the Stratford City project and the Olympic Park 'can be delivered and should be delivered together'.
The CPO should in fact help the Stratford City development because they too will benefit from services to the Olympic Park, such as road access, she added.
Construction on the Stratford City regeneration project in east London is due to start in late 2006 or early 2007, with completion of the development scheduled for 2020.
It plans to transform the 180-acre site of the former Stratford Rail Lands into a mixed-use development, including 4,500 new homes, office space, hotels and shops.