|John Grisham has sold more than 275 |
million books in his 25-year career
He earlier said some of those jailed may have had too much to drink and should have faced lesser penalties.
But on Thursday, Mr Grisham argued "anyone who harms a child for profit or pleasure... should be punished to the fullest extent of the law".
His initial comments angered child abuse charities and legal experts.
The American author, 59, posted the apology on his website as he prepares for the publication of a new legal thriller.
"My comments... were in no way intended to show sympathy for those convicted of sex crimes, especially the sexual molestation of children," he wrote. "I can think of nothing more despicable."
Mr Grisham, who has sold more than 275 million books during a 25-year career, initially made the comments in an interview with the UK newspaper The Daily Telegraph.
He launched a wide-ranging attack on America's judicial system for sending "too many people" to prison, focusing his anger on the length of imprisonment imposed on offenders who download images of children being sexually abused.
But campaigners criticised the writer for apparently offering an excuse for child abuse.
"Mr Grisham's comments send a dangerous message that 'just looking' at images online causes no harm," Jon Brown from the children's charity NSPCC told BBC News online.
"In fact, every image is a real child who has suffered and every time these images are clicked on or downloaded it creates demand that ultimately fuels more child abuse."
Meanwhile, London-based child abuse lawyer Dino Nocivelli urged the author to meet survivors of abuse "to educate himself and to truly understand the inappropriateness of his comments".
The US has the world's largest prison population, with about 2.2 million adults behind bars.
In 2012, close to 25% of the world's prisoners were held in American prisons despite the US accounting for just 5% of the world's population.
That means the US has 5 times as many prisoners per capita than the average country. It may not be because the US is sending more people to jail, but may have more to do with the very long sentences American judges hand out compared to the rest of the world - often several times what someone would get elsewhere.