Yesterday, she made public a series of e-mails on the matter, only to take them down from her Facebook page several hours later.
In the e-mails between her and Straits Times associate editor Ivan Fernandez, who was editing her columns, Dr Lee said she was "at odds" with her brother, Prime Minister Lee Hsien Loong.
Using her brother and the late Lee's initials, Dr Lee wrote to Fernandez: "HL has no qualms abusing his power to hv a commemoration just one year after LKY died, 'least (sic) we forget'.
"If the power that be wants to establish a dynasty, LKY's daughter will not allow LKY's name to be sullied by a dishonorable son."
Dr Lee's post prompted PM Lee to respond on his Facebook page several hours later. He said he was "deeply saddened" by his sister's charge, and added: "The accusations are completely untrue."
Last month, individuals and organisations, including grassroots groups, organised over 100 events to commemorate Singapore's first prime minister and remind themselves of his key values.
Yesterday, PM Lee said the Cabinet had discussed how Lee should be remembered, and he advised it be left to ground-up efforts and that these should be kept in proportion and be forward looking.
But Dr Lee, in an earlier Facebook post, said a picture of an art installation of 4,877 erasers in the likeness of Lee Kuan Yew's image, that was featured on the front page of ST on March 21, made her wince.
It prompted her to submit an article on the commemoration to ST, and she said that while the installation was well-meaning, she did not see the need for such commemorations so soon after his death.
Two days later, on March 23, Fernandez replied to Dr Lee with an edited version of her article, slated for publication on March 27.
She said it read well, but she wanted to wait until the day unfolded.
On March 25, Dr Lee submitted another version of her column, with substantial additions, and insisted on it being run unedited or she would post it online.
Fernandez rejected this, saying her paragraphs on how China's Mao Zedong and Britain's Winston Churchill were honoured after their deaths went off on a tangent.
Later that day, Dr Lee posted the article on her Facebook page.
In subsequent postings, she said ST was suppressing her views and denying her freedom of speech.
The paper responded in an editor's note last Tuesday saying her accusations that she was suppressed were unfounded. The paper said her column was being edited, as is done by all professional newspapers, and that it was "not an issue of freedom of expression, but a matter of upholding standards".
This sparked a series of online posts by Dr Lee, who said those who had edited her columns had been "commanded to edit certain issues out, and they are to (sic) timid to disobey, and too embarrassed by their timidness to tell me the truth".
Last Saturday, Fernandez wrote an article in the ST explaining why the paper declined to publish her column. Among other reasons, he revealed that the parts on Churchill and Mao had been plagiarised.
In her Facebook post releasing the e-mail exchange to show that Fernandez did not point out to her that she had plagiarised, she said she had not intended to do so, adding: "I simply forgot to acknowledge the source for information regarding Mao and Churchill."
Responding to her allegations, ST editor Warren Fernandez said yesterday: "Dr Lee's allegations are unfounded. ST had intended to run her commentary and our editors were working with her to get it ready for print. But some concerns arose, including over the plagiarised paragraphs. This was a serious matter, not least as our editors had spoken to her before about the pitfalls of copying material without attribution.
"Dr Lee now says this was unintended, as she 'forgot' to cite her sources, and besides, her end of exposing the government justified it anyway," he added.
"In addition to this, we found her ultimatum to print her piece unedited or she would go online, totally unacceptable. But before we could discuss this further, she went online, putting an end to any further engagement on the matter."