The Conservatives have said the reason some of their backers wanted to remain anonymous was that they feared they would lose government contracts.
David Cameron is under pressure to name past lenders
The party has agreed to name future lenders but is resisting calls by Labour to name past ones.
A spokeswoman said some lenders feared "malicious" ministers would cut off public sector work.
Labour's former general secretary wrote to backers saying any loans would not have to be declared, it has emerged.
But the party has since named all 12 backers, who lent it almost £14m before the last general election, after it emerged four of them had been nominated for peerages.
The Electoral Commission has written to the treasurers of all the main parties asking them to declare all loans which "are not on commercial terms", including those which "may be converted into a donation at a later stage".
They have until next Wednesday to respond.
A Tory spokesman said: "The Conservative Party has agreed to disclose the source of future loans as the Electoral Commission requested last week.
"In respect of past loans, these have been audited and fully comply with Electoral Commission rules but it would not be fair to apply new rules retrospectively - especially without the agreement of the people who made the loans."
She said some lenders wanted to remain anonymous because they "fear that ministers would be malicious and that public sector work that their businesses have might be affected unfairly".
Work and Pensions Secretary John Hutton has called on the Conservatives to "come clean" about its past lenders.
Mr Hutton said: "Labour has faced up to the need for greater transparency and published the names of everyone who has loaned the party money.
"Why is the Conservative Party still not publishing the names? Already the Shadow Attorney General Dominic Grieve has said the Tories should have 'complete transparency'.
"It is time for David Cameron to match his words on openness with actions to declare all Tory loans."
Labour's loans were made with interest rates of between 1% and 3% above the base rate.
Labour's then General Secretary, Matt Carter, sent letters to donors after the loans had been made.
The purpose was to "set out the legal terms upon which the Labour Party received the loans so as to ensure it was done in a fair and legal way, strictly within all legal guidelines," a Labour spokesman said.
Following the disclosure of the loans, Mr Blair announced plans to withdraw as prime minister from the process of nominations for honours. This did not affect his ability to create peers.
On Thursday, Rod Aldridge, the chairman of outsourcing firm Capita, said he was to step down over "spurious" claims his £1m loan to Labour had resulted in the group getting government contracts.
An inquiry into party funding has been launched by the influential constitutional affairs committee, who will also interview Tony Blair's chief fundraiser Lord Levy.
He will also face questioning from the public administration committee.