The communities secretary, Sajid Javid, is being accused of going "missing in action" and distorting business rate rises as he faces rancour from the Conservative backbenches over the increases.
It follows him writing to Tory MPs attaching a list of rate changes which apparently underestimate the rises in each constituency by between 5 and 7 percentage points.
The new business rates would be linked to property prices, which are higher in the Conservative heartland of the south east.
Controversy has been growing that retailers such as Amazon, which do not rely on "bricks-and-mortar" premises, are favoured and will see their rates drop.
When the row erupted, Javid was said to be on holiday. One senior government source told The Times: "Sajid got us into this mess and it has been left to the Treasury to try to clear it up."
Another told the paper: "There is a lot of unease about how this has all been handled. It hasn't helped that Saj and his team were absent all last week."
Javid's letter claimed, according to figures from the Department for Communities and Local Government (DCLG), that business rates would decrease in 259 out of 326 areas. However, rates will only drop in 135 areas and actually go up in 191.
Pressure will be building on Phillip Hammond to respond to the controversy in next month's Budget as Tory MPs have confronted the chancellor with details of how businesses in their constituencies will be affected.
The Telegraph reported that Hammond might try to help businesses hit hardest by the rates hike to appease Tory rebels. He has indicated that the system should be reformed in future to ensure online retailers pay a fairer share.
A Treasury source told the paper: "He's open to listening to the issues of those who are hardest hit, but there was no decision either way."
The DCLG said the analysis showing the alleged impact of the rises, carried out by international property consultants Gerald Eve, was "nonsense".
"This is yet more scaremongering when, in reality, businesses in 80% of council areas will see an average fall in their business rates bills," a DCLG spokesman said.