In October 2007, when the Northern Rock crisis was at its height, he said it was obvious to him he was spending most of his time in London and so he changed his second home to his Edinburgh property.
"If you look at how much I claimed in the last couple of years it is actually a lot less than it was in the past," he said.
On the service charge, he said he had been entitled to claim for it at the time, when he was living in the flat.
But he said it "ran ahead" six months - covering a period in which he had moved to Downing Street - and in hindsight, he did not want to be "gaining from something I shouldn't have".
"That's why I decided to repay that sum, I'm very sorry about it, I unreservedly apologise for it - it shouldn't have happened and that's why I've decided to repay that money."
Mr Darling also claimed on expenses for tax advice. He said any tax advice he received for personal tax had been paid for himself.
But he said MPs' office costs could be complicated as they were treated as MPs' own income for tax purposes and it was important to make sure his returns were completed accurately. He said he had paid tax on the value of the accountancy fees.
I think what matters is that the prime minister either backs him or sacks him
David Cameron Conservative leader
As a cabinet minister, and especially as chancellor, he said he wanted to "make sure I pay the correct amount of tax".
Asked if he would be remaining as chancellor, amid speculation he might be moved in an expected reshuffle, Mr Darling said it was for the prime minister to decide who is in the cabinet.
But he said it was "upsetting" when his personal integrity was "impugned".
"I have tried to behave properly, to do the right thing, the proper thing, throughout my time as a member of Parliament and as a minister."
But he said he understood why people were "thoroughly hacked off" about the expenses row.
The Liberal Democrats say that claims by the chancellor, as guardian of the public finances, must be above reproach and have called for him to go.
Treasury spokesman Vince Cable told BBC Scotland that the chancellor must be seen to have "moral authority, not just operating within technical rules, by the financial community and the country at large".
Conservative leader David Cameron told the BBC he thought Mr Darling was in "serious difficulties".
"I think what matters is that the prime minister either backs him or sacks him. I think this just leaving him to hang out to dry is very bad but I think it just strengthens my argument for a general election.
"If you start saying 'Well, why not get rid of the chancellor?', well - why not James Purnell, why not Geoff Hoon? I think what we need is the cleansing process of a general election where we all have to go back to our constituencies, we all have to explain ourselves and we let the public be the judge and the jury."
But the prime minister backed Mr Darling earlier, saying he had made an "inadvertent" mistake on the service charge and was doing a "great job" as chancellor.
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