However the trip at least began well, with the Queen being greeted warmly by the Sultan, cheered by thousands of children and piped by a guard of honour playing "Over The Sea To Skye".
She and the Duke of Edinburgh then took tea from English china in a white- and-gold chamber where the Queen and the Sultan were both seated on thrones. The guests were introduced to the Sultan's two wives, Paduka Seri Baginda Raja Isteri and Pengiran Isteri, a former air hostess, by whom he has 10 children.
In the Malaysian capital, Kuala Lumpur, however, where the Queen arrives on Sunday to close the Commonwealth Games, officials said threats had been made to bomb the main stadium.
But the biggest shadow over Malaysia is political - the struggle between the country's charismatic young politician Anwar Ibrahim and Dr Mahathir Mohamad, its anti-British Prime Minister.
At the opening ceremony last Friday, presided over by the Malaysian king and attended by Prince Edward, there was a theatrical performance that showed the peaceful Malaysian peoples being horribly overshadowed by the malign forces of Portuguese and British imperialism, represented by inflatable plastic dragons.
"There was a certain amount of gnashing of teeth," one Commonwealth diplomat said, "what with Prince Edward being there."
During the last two days of the state visit, before the Queen leaves next Wednesday, the focus will be on the increasingly heated political battle between Dr Mahathir and Mr Anwar, his former right-hand man, sacked two weeks ago as Deputy Prime Minister and Minister of Finance.
Devastatingly, for a devout Muslim, he has been accused of adultery, sodomy, consorting with prostitutes and even treason.
Mr Anwar has embarked on a campaign of reform, demanding greater freedom of the press, improved human rights and an end to political manipulation of the police and judiciary. His nightly speeches have attracted crowds as large as 50,000, and police say his arrest is imminent.
Only one thing appears to be guaranteeing his liberty: the Games, and the imminent arrival of the Queen. "I believe their timing will be perfect," he said of the police who might arrest him. "They will wait until Her Majesty leaves."Reuse content