Mr Lee and Suharto had a good personal relationship throughout their political careers, despite low points in bilateral ties.

One was the execution of two Indonesian marines in Singapore for the 1965 bombing of MacDonald House in Orchard Road, despite a direct appeal by Suharto.

However, Mr Lee’s gesture to lay flowers on the marines’ graves in 1973 helped soothe the tension and showed Singapore’s commitment to improving relations with Indonesia.

The “empat mata” meetings between Suharto and Mr Lee during Association of South-east Asian Nations and other meetings further helped build rapport and confidence.

Mr Lee wrote in his book From Third World To First: “Our friendship overcame the many prejudices between Singaporeans of Chinese descent and Indonesians. Throughout the 1970s and ’80s, we met almost every year to keep in touch, exchange views and discuss matters that cropped up.”

During the 1997-98 financial crisis and as the International Monetary Fund (IMF) put pressure on Indonesia to undertake structural reforms, Mr Lee was against sudden regime change in Indonesia. He believed discontinuity would worsen its already precarious situation.

Despite Suharto’s fall from power in 1998 and against popular opinion in Indonesia, Mr Lee saw him as a “patriot”.

Writing in From Third World To First, he viewed the change with concern and some sorrow: “It was an immense personal tragedy for a leader who had turned an impoverished Indonesia of 1965 into an emerging tiger economy, educated his people and built the infrastructure for Indonesia’s continued development.”

In a display of personal diplomacy, Mr Lee made a trip to see Suharto shortly before the Indonesian leader died in 2008.

In contrast, Mr Lee’s views of Suharto’s successors were mixed. His initial reaction to the prospect that Mr B J Habibie, who served as Vice-President to Suharto, would take over from the latter was less than positive. But later, even after Mr Habibie remarked that Singapore was a “little red dot in a sea of green”, Mr Lee reassessed him to be “highly intelligent, but mercurial and voluble”, as he wrote in From Third World To First.

Mr Lee also credited Mr Habibie for Indonesia’s decentralisation efforts that empowered the districts and municipalities, which helped prevent separatist tendencies from mushrooming.

Later, in Tom Plate’s 2010 Conversations With Lee Kuan Yew, Mr Lee would say of Indonesia: “Successor Habibie made a mess of it. Then Gus Dur made a bigger mess. Megawati calmed it down. SBY (Susilo Bambang Yudhoyono) has improved it slightly, but there’s a long way to go.”

Beyond personalities, Mr Lee also made a number of visits to the country to meet a broad range of political actors in order to better understand post-Suharto Indonesia. This habit of reaching out to senior Indonesian leaders continues today — Prime Minister Lee Hsien Loong held retreats with his Indonesian counterpart in 2010, 2012 and 2013.

Pushpanathan Sundram is former deputy secretary-general of ASEAN for ASEAN Economic Community, managing director at EAS Strategic Advice, Asia and senior research fellow at the Singapore Institute of International Affairs (SIIA). Simon Tay is chairman of SIIA and author of Asia Alone: The Dangerous Post-Crisis Divide from America.