A lack of consensus with the club over the proceeds of any sale may be the reason for the ministers' concern.
The takeover of the European champion could be timed out if deadlines are not met, according to a UK government insider.
Todd Boehly, co-owner of the LA Dodgers baseball team, is one of the investors in the deal.
The club was put up for sale before Roman Abramovich was sanctioned for his alleged links to Russian president Putin.
A senior source in the government said there was now a serious concern that the billionaire was willing to let the club go under.
The approval of ministers and the English football authorities is required for any takeover of the club.
When the club is sold, the loan will not be repaid, according to the owner. A spokesman for the billionaire confirmed that he remains committed to making sure the proceeds from the sale go to good causes.
The club has a complicated ownership structure, with parent company Fordstam having a large debt to a Jersey-based company.
There are two big sticking points - where exactly the proceeds of the sale will be held and what legal guarantees the government will give about the money going to good causes.
Despite committing to all proceeds going to good causes in public, Abramovich seems unwilling to give the same legal commitments, which would have backed up his public statements of about a week ago.
A deal which would allow the cash to be diverted during the deal would be a violation of sanctions and is seen as a red line for ministers.
There are deadlines at the end of this month and the beginning of June, which could see the club ejected from European competition or the premier league entirely. A good portion of the sale needs to be done this week or next.
The licenses needed to compete next season would need to be granted by the premier league by early June, so any sale would need to be completed by that time.
The government is said to have proposed a two-stage process where the money from any sale would be held in a managed account and only released once it is satisfied that a charitable foundation is ready.
A spokesman for Mr. Abramovich has been approached for comment.
A source close to the Boehly consortium told the BBC that the group is committed to buying a club.
They are delighted that their plans have been accepted by the club, and they are happy with the constructive conversations they have had with the government and football authorities.
The proceeds of the sale are a matter for the seller and the government.