Control of tracks and stations will pass to a new firm
The Sunday Times newspaper claimed to have seen documents that suggested legal papers to close down the company were drawn up more than a week before the announcement, while shareholders were still trading in the company's stock.
The Conservatives have pressed Mr Byers "to come clean" on the issue and to resign and Railtrack chairman John Robinson wants an independent inquiry into the events leading up to the company going into administration.
Mr Byers said the supposed leaked document seen by the newspaper were in fact contingency plans being drawn up for Railtrack.
Contingency plans
It was part of the set of draft rules that had only been finalised on 5 October and had been available for MPs to see in the Commons library since 8 October, said Mr Byers.
He continued: "It could not have been drawn up overnight once a decision had been taken."
Mr Byers accused the Tories of being unable to come to terms with the fact that their "failed" privatisation of Railtrack had come to an end.
He said that the date on the top of the paper was the day the contingency plans document was being prepared by the Stationery Office.
Exploring the contingency plans was the best way of protecting passenger interests, argued Mr Byers.
Mr Byers has already told the House of Commons he had had discussions with the accountants Ernst and Young about Railtrack's future as early as 23 August.
His statement to the Commons comes after shadow transport secretary Theresa May put down a private notice question in Parliament on the latest allegations.
Document dates
Ms May told MPs on Monday the government's whole credibility had been undermined by the handling of the Railtrack issue.
"As more and more pieces of the jigsaw come together, it now appears that far from this being a decision made during the course of the afternoon of 5 October, as he claimed, this was a drawn out act of wilful destruction by Stephen Byers.
"It is clear that he was bent on destroying Railtrack from the start.
"Sadly, while Mr Byers had already decided to wind up Railtrack, thousands of employees of Railtrack were investing more of their hard-earned life savings in the company."
Claiming that Mr Byers was a huge obstacle to railway investment, she added: "He must go."
But Liberal Democrat transport spokesman Don Foster directed his fire at the Tories, whom he accused of doing "nothing more than whingeing on behalf of the shareholders who since May 1996 have received £700m in share dividends".
Mr Byers said he had taken the decision to wind up the company on 5 October.
The document at the centre of the statutory instrument to put the company into administration, was dated 6 October to come into effect on 7 October.
But the Sunday Times claimed the document was also dated 28 September - suggesting a copy was faxed on that day.
Mr Byers said that date was instead the day the document was to be printed by the government Stationery Office.
Company plans
Ministers have promised to transfer control of Britain's 23,000 miles of track and 2,500 stations from Railtrack to a new firm within six months.
Mr Byers has proposed a not-for-profit company.
Railtrack's chairman John Robinson renewed his attack on the government shortly before the Commons statement.
Calling for an inquiry, Mr Robinson said: "Contingency plans are one thing, but what we have here is the suggestion that final documents had been circulated among officials that would shortly wipe out Railtrack shareholders' equity."