Outnumbered police officers were turning away mourners at the City Hall metro station next to the Padang, an open field where the mourners were queueing to enter the legislature.
"The Padang queue is closed for public safety. Please go back home," a police officer said using a loudhailer.
A government statement said that as of 11 pm, more than 290,000 people had paid their respects to Lee since his casket was brought to parliament's main lobby on Wednesday after a private family wake.
Thousands more were massed in long, snaking lines, packed like cattle at some points, despite waiting times of up to 10 hours.
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The statement said that although the government would like to accommodate more people, they were "temporarily" suspending the queue for the safety and well-being of those in line.
"We will inform the public when the queue is open again," it said, urging people to pay homage at 18 locations around the island.
Until the suspension, the queue ran for 24 hours following an overwhelming show of sympathy for the revered patriarch who transformed Singapore from a British colonial outpost into one of Asia's wealthiest societies in just 30 years.
"Yes, I am disappointed. We made plans to come on Friday night because we are all working," said sales executive Shawna Tseng, 27.
"We won't be turning back. We will wait until they repoen the line," she told AFP after unsuccessfully trying to negotiate entry with a stern police commando, who curtly replied "my advice to you is to go home now".
The city-state, famous for its clockwork handling of major events like the night-time Singapore Grand Prix, seemed unprepared for the scale of the outpouring of grief.
"I am deeply moved by the overwhelming response of people wanting to visit my father's Lying in State at Parliament House," Prime Minister Lee Hsien Loong said on Facebook.
He announced that a live video feed of the flow of mourners viewing the casket inside the parliament's lobby had been put up on YouTube.
Lee has been lying in state since Wednesday and the public was supposed to have until 8 pm (1200 GMT) tomorrow to pay their respects.