Islamist militants from those three countries have a record of working together and several Malaysians are known to have carried out suicide attacks in the Middle East.
Indonesia has seen attacks by Islamist militants before, but a coordinated assault by a team of suicide bombers and gunmen is unprecedented and has echoes of the sieges seen in Mumbai seven years ago and in Paris last November.
In a recent blog post, entitled "Lessons from the Paris Attacks", Naim had urged his Indonesian audience to study the planning, targeting, timing, coordination, security and courage of the jihadis in the French capital.
Australian Attorney-General George Brandis, who was in Jakarta recently to bolster security coordination, told the Australian newspaper he had "no doubt" Islamic State was seeking to establish a "distant caliphate" in Indonesia.
The country had been on edge for weeks over the threat posed by Islamist militants, and counter-terrorism police had rounded up about 20 people with suspected links to Islamic State.
There was a spate of militant attacks in Indonesia in the 2000s, the deadliest of which was a nightclub bombing on Bali that killed 202 people, most of them tourists.
Police have been largely successful in destroying domestic militant cells since then, but officials have more recently been worrying about a resurgence inspired by Islamic State.
Many experts believe that Indonesia, a vibrant democracy where the vast majority of Muslims practise a moderate form of Islam, is not likely to be tipped into a cauldron of militancy.
"It is true that a tiny number of the country's army of poorly educated, desperately underemployed young men are attracted to the guts-and-glory narrative spun by ISIS," author and long-time Indonesia foreign correspondent Elizabeth Pisani wrote in the Financial Times. "But their discontent is based on economic rather than religious or political marginalisation."