For once, Singapore prime minister Lee Hsien Loong can’t agree with his father, minister mentor Lee Kuan Yew. He had to distance himself from the patriarch to douse a controversy over race and religion.

The blunt, no-nonsense 87-year-old former prime minister riled the Muslim minority with comments he made in his new book, Hard Truths to Keep Singapore Going. The book, presented in a question and answer format, quotes him as saying: “I would say, today, we can integrate all religions and races except Islam.”  He added: “I think the Muslims socially do not cause any trouble, but they are distinct and separate.”  He blamed the Arab world and growing Islamization, saying: ”I do not want to offend the Muslim community. I think we were progressing very nicely until the surge of Islam came, and if you asked me for my observations, the other communities have easier integration – friends, intermarriages and so on, Indians with Chinese, Chinese with Indians – than Muslims. That’s the result of the surge from the Arab states.”

Asked what Muslims could do to integrate, he said: “Be less strict on Islamic observances and say, ‘Okay, I’ll eat with you.’” He also said the Malay Muslims would never close the gap in education with the Indians and the Chinese, “because as they improve, the others also improve”.

No wonder the Muslims are upset and the prime minister is trying to appease them, saying he doesn’t agree with his father. “I think Singapore Muslims have made a special effort to try and bridge the links between them and the other communities,” he said.  He was responding to aggrieved Muslims, who wanted to know if the government shared his father’s views. The minister in charge of Muslim Affairs, Yaacob Ibrahim, also said the elder Lee’s views “may not be accurate now”. “We can be both religious and patriotic at the same time,” he added.

The government’s conciliatory remarks have not reassured everyone. “There goes the Malay vote,” commented a blogger, convinced the controversy will hurt the ruling People’s Action Party in the coming elections. The island is expected to go to the polls some time after the budget is presented this month. The elder Lee, or MM Lee, as the minister mentor is called, has been long enough in politics to know the power of words. So why did he rile the Muslims with an election coming? The Muslims – Malays mostly, but also including Indians and Chinese – make up 15 per cent of the resident population. They are a bigger group than the Hindus (5 per cent) and the Taoists (11 per cent) though smaller than the Christians (18 per cent) and the Buddhists (33 per cent) and those who don’t subscribe to any religion (over 17 per cent).

The controversy not only ruffles the racial and religious harmony the government is keen to maintain but goes against what Lee Kuan Yew himself stands for. The man who led Singapore to independence also worked hard for national integration. It was under his leadership that Singapore adopted a Malay national anthem, Majulah Singapore (Onward Singapore). He was the prime minister when the Malay Yusof bin Ishak became the country’s first president. The massive public housing projects he launched,  in which more than 80 per cent of the Singaporeans now live, housed the different races under the same roofs. Malays, Indians and Chinese live in the same apartment blocks – there are no ethnic enclaves in Singapore.

It’s true the wars in Iraq and Afghanistan have cast their shadows on Singapore and the surrounding region. Southeast Asia has its own al-Qaeda, the Jemaah Islamiah (JI), which carried out the Bali bombings killing more than 200 people in 2002 and several other terror attacks but was foiled in a bid to strike Singapore. Singaporean JI operative Mas Selamat Kasturi, trained in Afghanistan, made the headlines when he escaped from prison in Singapore in February 2008. He was recaptured in Malaysia after more than a year. His brother, sister-in-law and niece were sentenced to prison for helping him escape.

But that was an isolated incident. Singapore remains peaceful and prosperous, but a cover-up is under way. I can see it in Siti (not her real name), a dear friend of my wife. We have known her for nearly 20 years. Back then she was a modish young woman who dressed in jeans and tops. Now she is a middle-aged matron who covers herself from head to toe. Her generous figure is ensconced in colourful baju kurungs – a full-length dress consisting of a full-sleeved blouse and skirt – her head modestly covered  in a tudung, a headscarf. Fewer Muslim women are seen in Western dress. It used to be said every Malay boy plays the guitar. The Mat Roks are still around, zooming around on bikes in bright T-shirts. But the Minahs – their girls – are more likely to wear baju kurungs.

Siti has abandoned Western dress, but she has enrolled her grand-daughter in an expensive kindergarten for international students instead of sending her to the local preschool. She wants the child to speak good English. That’s a language more widely spoken by the Indians and the Chinese. Half the Indian and Chinese children speak English at home, but only 26 per cent of the Malays, according to the 2010 census. So, yes, there are differences, but irreconcilable differences? No. As the song goes, “One people, one nation, one Singapore/ That’s the way that we will be forevermore.”