The Council of Mortgage Lenders in Scotland said its members would almost certainly pass on to customers any increased costs brought about by changes to the current system.
The body also said it feared some lenders could pull out of Scotland if the new rules got the go-ahead.
Presently lenders and borrowers can share legal representation, drastically cutting legal fees. This situation also applies in England and Wales.
Changes have been proposed by the Law Society of Scotland, which in a consultation document said "every solicitor's client is entitled to, and must receive, independent advice focused on their best interests".
The Law Society said separate representation would further remove any potential conflict of interest in the house purchase process and need not lead to higher consumer costs, as the lenders did not have to pass those charges on.
But CML Scotland disagreed, warning lenders would get their money back from consumers somehow.
"It (the Law Society proposal) suggests that these are the costs of the lender in satisfying themselves as to their own lending risk and it is for lenders to decide whether they are prepared to absorb them or pass them on to the borrower," it said.
"Clearly if lenders did not lend, these are costs which they would not incur. In our view, they are perfectly entitled to pass them on to borrowers.
"If, as the LSS has previously suggested, lenders are prohibited from recovering these costs from the borrower, this will simply mean that lenders will recover their costs through interest margins and this will result in differential pricing between Scotland and the rest of the UK."
CML feared the changes would have a huge impact on the marketplace, and warned in a memo to the Law Society: "Some lenders, particularly those with a small market share in Scotland, may decide that the one-off costs of preparing for compulsory separate representation are not justified and may withdraw from lending in Scotland, thus reducing mortgage choice for consumers in Scotland."
The proposals were formed four years after home reports, costing up to £800 each, were introduced, requiring sellers to provide a single survey for potential buyers.
CML has told the Law Society that feedback from members showed they would need at least 12 months to implement the changes - and that some might withdraw temporarily from lending in Scotland until they developed systems to cope.
It said others might choose to use manual workarounds, which could limit their ability to deal with high volumes of applications, and which could also be prone to errors.
CML Scotland said: "The position of the LSS is in direct contrast to the Law Society of England and Wales, which have made clear that they want to see the same solicitor acting for borrower and lender in most domestic transactions.
"We do see the value of separate representation, but only where particular risk factors are identified in individual transactions and in cases where the borrower and lender client's choice of solicitor differs."
The Law Society of Scotland admitted its survey on the issue showed "the jury is out" on whether its members would vote for the change at a special general meeting next month. It showed 49% were in favour and 51% against the proposed rule change.