They warned that by Friday afternoon the queuing time to enter Parliament House was nine hours.
Some 250,000 people have already visited to pay respects to Mr Lee, who died on Monday aged 91.
A state funeral will be held on Sunday, with foreign dignitaries from around the world expected to attend.
Authorities said in a statement that members of the public were “strongly advised” not to join the queue now, and redirected them to smaller tribute sites set up around the island.
Public viewing, which has been open all day and all night since Wednesday, will end on Saturday night.
Officials were caught off-guard by the overwhelming crowds that showed up on Wednesday when public viewing began, with the queue snaking through the city centre.
The line has since been moved to the Padang, a large field used in central Singapore for parades and cricket matches, where tents and crowd control barricades have been set up
Water and umbrellas were distributed to those waiting under the sweltering heat.
Workers stand next to boxes of water for members of the public who have been queuing up to pay their respects to Singapore’s late former prime minister Lee Kuan Yew at Parliament house where he lies in state in Singapore on 27 March 2015
Mr Lee was the country’s first prime minister and led Singapore to independence in 1965. He was hugely respected by Singaporeans.
Mourners with infants pay their respects to Singapore’s late former prime minister Lee Kuan Yew where he lies in state at Parliament House in Singapore on 27 March 2015.
He will lie in state until Sunday morning, when his body will be moved to a cultural centre in the west of the city for his funeral. The funeral procession will wind through the city centre and his Tanjong Pagar constituency on the edge of the business district.
Vigil guards stand as mourners pay they respects to Singapore’s late former prime minister Lee Kuan Yew where he lies in state at Parliament House in Singapore on March 27, 2015
Past and present world leaders have arrived in Singapore to pay their respects during the public viewing, including former Indonesian President Susilo Bambang Yudhoyono.
Former Indonesian president Susilo Bambang Yudhoyono and his wife Kristiani Herawati pay their respects to the late first prime minister Lee Kuan Yew of Singapore at the Parliament House in Singapore 27 March 2015
Those attending the funeral include UK House of Commons leader William Hague; Indonesian President Joko Widodo; Malaysia’s King Abdul Halim; India’s Prime Minister Narendra Modi; Japanese Prime Minister Shinzo Abe; South Korea’s President Park Geun-hye and Australian Prime Minister Tony Abbott.
The US will be represented by former President Bill Clinton and former Secretary of State Henry Kissinger, while China has sent Vice-President Li Yuanchao.