"But they have, and we must learn the right lessons from them, get to the root of the problems, and put things right," said Lee on Sunday (Nov 19) at the annual People's Action Party convention here.
Singapore's MRT network has been hit by a spate of woes, including the train collision at Joo Koon last week which left 36 people injured.
Lee said such disruptions "loom large in the public consciousness", and are a reason why the public does not feel that rail reliability has improved even though statistics show there are "fewer delays and breakdowns than before".
He stressed that improving Singapore's infrastructure is a priority, especially its public transport system. Commuters should eventually see better reliability when major projects like resignalling are fully completed, he added.
The authorities will continue expanding the public transport network as well, and make other major social and infrastructure investments, he said, adding that taxes will be raised as spending needs grow.
Lee noted that improving train reliability is a "very complicated problem".
Apart from the technical issues, there is also a need to strengthen the train operators as well to deliver consistent high performance, he said. Engineering and maintenance teams must be reinforced, and morale maintained.
The ongoing upgrading of the signalling systems on the older North-South and East-West lines will cause their own set of delays, he said.
"Once the signalling upgrade is fully completed, hopefully within a year's time, these delays should go away," he said.
He added: "The best thing we can now do is to give our transport team the time and the space to work these problems out."
He said Singapore already has a "first-class transport system", its reliability comparable to other cities' in the world.
The top cities in the world for reliability are Hong Kong, Taipei, Los Angeles, and Singapore, he added, with trains being on time over 99% of the time.
"The Transport Minister has one of the toughest jobs in Cabinet ... I want Boon Wan and his team to know that they have our full confidence," he said.
Besides improving train reliability, the authorities will also expand the transport network with major investments such as the High Speed Rail to Kuala Lumpur, and development of other regional centres such as Woodlands and Punggol, said Lee.
Singapore will also double the capacities of its air and sea ports with Changi's Terminal 5 and a megaport in Tuas. The megaport will open up the Great Southern Waterfront for longer-term development, a new area thrice the size of Marina Bay, he said.
"But the investments and social spending are costly, and we have to make sure that we can afford them," he said.
He added that Government spending will rise further, spending needs will grow, and raising taxes, as finance minister Heng Swee Keat said, is "not a matter of whether, but when".
Besides Lee, Transport Minister Khaw Boon Wan also brought up rail issues at the event at the Big Box in Jurong on Sunday.
Khaw, who is the PAP chairman, promised commuters in an earlier speech that the government would complete its work on the MRT lines.
He added that he had arrived at the awards and convention via the North-South Line, and commuters had come forward to encourage him.
"I thanked them and I promised them, we shall complete this work. And we will. This is a promise," he said. - The Straits Times/Asia News Network