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The US is accusing Indonesia of dragging its feet in tracking down suspected Islamic terrorists, amid fears that the vast South-east Asian nation may become a hideout for supporters of Osama bin Laden.

After several weeks of behind-the-scenes lobbying, American complaints were made explicit last week by the outgoing head of the US Pacific Command, Admiral Dennis Blair. "Indonesia has not aggressively investigated domestic elements that are sympathetic to the aims of al-Qa'ida," said Admiral Blair, at a Senate hearing. "Indonesia's very geography makes it vulnerable to terrorist penetration... Indonesia's security apparatus does not have full control of its borders."

His remarks reflect the belief that Indonesia has become the weak link in a co-ordinated campaign against extremist operations in the region, which has resulted in arrests of alleged terrorists in Malaysia, Singapore and the Philippines. Indonesia insists that it is doing all it can, and that it will not jeopardise its young democracy by arresting people merely on suspicion of terrorism because the US wills it.

"The relationship must be of equal partners," said the Indonesian army's deputy chief of staff, General Kiki Syahnakri. "Not as one acting as the superpower, as the world's police officer, and the other one ordered around."

Islamic extremists from many Asian and Middle Eastern countries converged in large numbers on the Indonesian province of Maluku, formerly known as the Spice Islands, where Christians and Muslims have been engaged in a murderous conflict since 1999. In the remote jungles of Papua province, in the far east of Indonesia, a group named Laskar Jihad, which fought in Maluku, is reported to have become active. Last month a suspected member of the group was arrested in possession of bombs, guns and swords.

American frustration is focused on one man in particular – Riduan Isamuddin, known as Hambali, a 37-year-old Indonesian alleged to be "operations director" for al-Qa'ida's South-east Asian network. The US insists he directed a plan to use weed-killer bombs to blow up Western missions, including the American Embassy, and US naval ships in Singapore.

"Seven trucks, three tonnes each, moving simultaneously to seven different targets in Singapore – boom!" said Singapore's Prime Minister, Goh Chok Tong, describing the planned attack. "I don't know how many thousands would have been killed."

Last month, an Indonesian accused of lethal bomb explosions in Manila metro stations went on trial in the Philippines capital. But, despite President Megawati Sukarnoputri's avowals of support for the war on terror, no such developments have taken place in Indonesia.

The 3,000-mile-wide archipelago of 14,000 islands, most of them uninhabited, has always been a place of sanctuary for pirates, rebels and outlaws. In some parts of the country, central control has broken down completely.