Labour has called on him to step down after he appeared to suggest some rapes were less serious than others.
Mr Clarke said he was simply describing a "long-standing factual situation" in which sentences differ depending on the circumstances of a particular rape.
But he said he would "choose my words more carefully in the future".
Mr Clarke will face more questions about his remarks on BBC's Question Time later, which will be broadcast from Wormwood Scrubs in west London, with inmates included in the audience.
The row began on Wednesday morning when the justice secretary gave an interview to BBC Radio 5 live about proposals to halve jail terms for people who plead guilty early, including rapists.
Currently, offenders who plead guilty at the earliest opportunity are entitled to a reduction in their sentence up to a maximum of 33%. The government is consulting on extending that to 50%.
BBC home affairs correspondent Danny Shaw says the proposal is absolutely crucial to the Ministry of Justice's cost-cutting plans.
The department estimates it would save 3,400 prison places - and ?130m - a year by 2015. That saving represents 62% of the ?210m a year it has promised to cut.
'Disgraceful'During the BBC interview, Mr Clarke disputed reports that the average sentence for rape was five years and insisted that "serious rape" attracted a much longer term.
Continue reading the main story Norman Smith Chief political correspondent, BBC Radio 4Ken Clarke is probably safe in his job for now.
In part that's because the Labour leader demanded he be sacked, thereby making it almost impossible for Mr Cameron to offer up his scalp.
Mr Cameron is also hugely averse to being pushed around by the media.
At the same time Mr Clarke adds ballast and balance to a cabinet which would otherwise be bereft of that rare breed - one-nation, pro-European Tories.
Longer term, however, there will be some in government who think the old political bruiser should move on.
Not just because of today's headlines, but because his manner and tone jar with the more modern, metropolitan image of the Conservative Party that David Cameron has tried to create.
Labour leader Ed Miliband later told MPs it suggested there were "other categories of rape" and called on him to resign.He was also confronted on the radio phone-in show by sex attack victim Gabrielle Browne.
Mrs Browne, who has waived her right to anonymity, later told the Daily Telegraph, his comments were "disgraceful".
On Thursday morning Mr Clarke said he had no intention of changing the sentencing guidelines on rape but it had long been the case that "different rapes get different lengths of sentences from judges".
"People are punished more if they make the witness go through the ordeal again, but that's a very long-standing arrangement which has always applied to all crimes.
"If I caused genuine offence to anybody by explaining that long-standing factual situation, then I must have made a very poor choice of words, so I will try to choose my words more carefully in the future."
He again refused to apologise or resign, saying: "I've encountered ministers resigning for proposals they haven't made, but to resign for proposals I've never made or thought of making would be just a little odd, I think."
Mr Clarke has written to Mrs Browne to say he believes "all rape is extremely serious", adding: "I am sorry if my comments gave you any other impression or upset you."
He also told her he wanted to hear her views "on how the criminal justice system can be made more effective" and invited her to meet him next week.
'Clearly regrettable'After Mr Clarke's radio comments, David Cameron told MPs rape was "one of the most serious crimes that there is and it should be met with proper punishment" and the "real disgrace" was that only 6% of reported rape cases ended in a conviction.
The prime minister's spokesman said it was "clearly regrettable" if anybody had been offended by Mr Clarke's comments.
He added that no final decision had yet been taken on whether to increase the maximum sentence discount for a guilty plea, saying: "We are not setting out the policy imminently and clearly we continue to listen to people's views."Labour has called for the idea to be scrapped, and the BBC's political correspondent Ross Hawkins said there were growing doubts about whether it could survive the current row.
Transport Secretary Philip Hammond told the BBC: "Ken is doing a very difficult job in very difficult circumstances.
"What the justice secretary is looking for is a practical way of getting more rapists convicted and that's why he's floating an idea - and it is only an idea - for consultation about sentencing discounts that would encourage more people to plead guilty early in the process."
But the official body which issues sentencing guidelines in England and Wales has said there is "little evidence" that increasing the reduction in term for an early guilty plea would encourage more offenders to admit their guilt.
The Sentencing Council also said it was unable to identify any jurisdiction in the world where the sentence discount was "significantly higher" than 35%.
Ministry of Justice officials estimate that if the sentencing proposal was to be implemented, average discounts would go up from 25% to 34%.
The Question Time audience will include 10 inmates and 10 prison staff as well as 100 members of the public.
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