Southeast Asian Games chiefs on Thursday played down "hiccups" at the event as they revealed that 16 Malaysian athletes had been hit by food poisoning in the competition's latest mishap.

One of the 16 was hospitalised and a swimmer was forced to miss a race after the athletes, who are all staying at the same hotel, fell ill on Wednesday, officials said.

Among other incidents, an upside-down flag caused fury in Indonesia and squash players from Myanmar were injured in a bus crash.

But SEA Games Federation president Tunku Imran Tuanku Ja'afar said some problems were to be expected at an event which is being run on a tight budget.

"It's run by very senior people in government but it's the implementation perhaps lower down and a lot of inexperience of Games that has caused some hiccups along the way," he said.

Officials said they were still trying to identify the source of the food poisoning, which left one athlete in hospital and 15 confined to their hotel.

Few other details were released but Low Beng Choo, secretary of the Games' sports and technical committee, said those affected had been asked not to compete until they recover.

"One went into hospital because we wanted to be very sure it was nothing very serious... it wasn't as if it was an emergency. The rest of them are resting in the hotel," said Low.

She added: "One of the swimmers missed an event. We asked him not to compete... in the interests of the athletes we have told the athletes not to compete."

- 'These things happen' -

The outbreak is not the first problem at the biennial SEA Games, which has 11 nations competing in a diverse array of sports from swimming to wushu, and still has nearly a week to run.

Organisers mistakenly printed Indonesia's flag upside-down in a commemorative booklet, prompting protests and revenge hacking attacks by Indonesian activists.

Imran said organisers were reprinting 8,000 copies of the magazine, adding: "Of course it's inexcusable for any flag of any country to be wrong. But these things happen, there are human beings somewhere that do make mistakes."

Among a litany of transport incidents, eight people suffered minor injuries in a bus crash, forcing two squash players from Myanmar to pull out of their doubles matches.

Myanmar's women's football team was stranded when their bus driver was arrested for stealing a watch, and on several occasions athletes have been late for competition after drivers lost their way.

"The transportation hasn't been perfect -- we believe it could be better and should be better," said Imran.

Two Myanmar football fans were beaten up after a match against Malaysia, and the home fans were also condemned for chanting "Singapore dogs" during another game.

Low said the SEA Games Federation was meeting Malaysia's football association to discuss tightening security before the home side's semi-final on Saturday.

Separately, Indonesia's women's sepak takraw team walked out in a protest over judging, and the men's and women's squash doubles finals had to be moved after the centre court surface was found to be too slippery.