According to the firm, 240,000 companies have deferred a total of £4.2bn in tax and 5% of those are potentially not in a position to be able to repay HMRC.
Nick Hood, chairman of Begbies Traynor, said: "It is a fantastic initiative for many of those involved. However, due to the sheer volume of applicants, there are a number of firms that should not have been supported.
"For these companies, rather than being a lifeline, [the scheme] has just postponed the evil day."
Begbies Traynor's warning came as the company released its Red Flag statistics, a monitor of companies facing significant and critical financial problems.
Significant problems are defined as those companies with either court action and/or poor, very poor, insolvent or out of date accounts. Critical problems are those with CCJs totalling £5,000 and/or a winding-up petition lodged against them.
Overall, the number of companies facing significant and critical financial problems had fallen by 14% in the final quarter of 2009 compared with the third quarter, but had risen by 6% year on year.
The print and packaging sector was in-line with the trend, recording a 17% year-on-year fall, but a surprise 5% increase on the previous quarter, despite the fact that the final quarter of the year is traditionally a busy period for the sector.
Up to 12,000 companies in tax deferral scheme 'may fail in 2010'
As many as 12,000 companies involved in the government's Time to Pay tax deferral scheme are in danger of collapsing this year, Begbies Traynor has warned.
