Lee and the two younger children of Lee Kuan Yew, Singapore's founding leader, have since last month been waging a bitter war of words on social media over their revered father's legacy, an unprecedented spectacle in a nation long used to censorship and libel suits against critics of the family.
"Their allegations are entirely baseless," Lee told a regularly scheduled session of parliament.
His sister Wei Ling and brother Hsien Yang accuse the premier of exploiting their father's legacy for his own political agenda, and seeking to groom his son to one day become leader of the city-state.
The prime minister called for an open debate in parliament after the attacks on Facebook against him and his wife Ho Ching, who heads state investment fund Temasek Holdings.
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Lee, who had earlier apologised to the nation for the open squabbling and admitted it had damaged Singapore's reputation, today firmly rejected the claims in a statement to the legislature.
"Unrebutted, they can affect Singaporeans' confidence in the government."
He added that Singaporeans were "tired of the subject, and wish it would end. I too am upset that things have reached this state".
At the centre of the dispute is the bungalow which the patriarch wanted destroyed after he passed away to prevent the creation of a personality cult.
The siblings said the prime minister is attempting to block the house's demolition to exploit their father's legacy, including grooming his own son to be a third-generation leader -- a charge Lee and his wife denied.
The patriarch served as prime minister from 1959 to 1990, and the current leader has been in power since 2004. The city-state has had only one other prime minister, Goh Chok Tong.