Singapore Prime Minister Lee Hsien Loong's younger brother and sister said on Wednesday that they have lost confidence in the nation's leader and fear "the use of the organs of the state against us."

"We are concerned that the system has few checks and balances to prevent the abuse of government. We feel big brother omnipresent," Lee Wei Ling and Lee Hsien Yang said in a joint news release and an accompanying longer statement issued at 2 am Singapore time on Wednesday.

As a result, Lee Hsien Yang, and his wife Suet Fern, would be leaving Singapore. "I have no desire to leave. Hsien Loong is the only reason for my departure," he said.

Lee Hsien Yang told Reuters he still remained in Singapore as of early Wednesday morning but said he was planning to leave "for the foreseeable future." He is a businessman and is currently the chairman of the Civil Aviation Authority of Singapore.

The siblings provided no specific evidence of action by the Singapore government against them. Reuters was unable to independently verify the accusations.

In a statement, the prime minister denied the allegations made by his siblings, and said he was very disappointed that they have chosen to publicise private family matters.

At the heart of the family dispute is the future of the house in which their father, Lee Kuan Yew, lived for most of his life. He was the first Prime Minister of Singapore and ruled the country for three decades.

Lee died in 2015, and according to the younger siblings wanted the home demolished rather than turned into a monument. They claim that the prime minister and his wife, Ho Ching, had opposed this wish.

The younger siblings accused the prime minister of wanting to “milk Lee Kuan Yew’s legacy for their own political purposes.” They said that they believed the prime minister and his wife, Ho Ching, “harbour political ambitions for their son, Li Hongyi.”

It is the second time in 15 months that the issue has exploded into public view. In April 2016, Lee Wei Ling accused the prime minister of abusing his power.

This time the involvement of both siblings, and Lee Hsien Yang's decision to leave the city state have taken it to a new level.

In his statement, Prime Minister Lee said he and his wife “especially” denied the allegation that they had political ambitions for their son, saying it was “absurd.”.

He said he would continue to uphold meritocracy as a fundamental value of Singaporean society.

"While siblings may have differences, I believe that any such differences should stay in the family," said Lee, who is overseas on holiday with his family.

"Since my father’s passing in March 2015, as the eldest son I have tried my best to resolve the issues among us within the family, out of respect for our parents... My siblings’ statement has hurt our father’s legacy. I will do my utmost to continue to do right by my parents."

The prime minister said he will consider the matter further when he returns to Singapore this weekend.