Wilson, a member of the winning women’s 4×100-metre freestyle relay team, was thought to have been suffering from appendicitis this morning, according to Fairfax Media.

However she was later cleared of the condition and was expected to make a second chartered flight.

Barratt was also still hopeful of making the second flight home, despite contracting pneumonia after the rain-affected closing ceremony.

The Rio Games were due to be Barratt’s last after also representing Australia in Beijing and London.

Bronte Barratt, left, with fellow silver medalists Emma McKeon, Tamsin Cook and Leah Neale after the women’s 4x200m Freestyle relay final. Photo: BERND THISSEN / EPA

The news of the duo in hospital came after it emerged Cate Campbell will undergo a second surgery on a hernia within 12 months on her arrival back in Australia.

The 100m world champion developed a hernia three months ago, but is refusing to blame it for her disappointing Rio results, according to News Corp.

Campbell came away with a gold in the women’s 4x100m relay, and silver in the medley relay, but failed to score an individual medal.

After a final night of celebrations in Rio de Janeiro, most Australian athletes this morning caught the first of two specially chartered flights home.

A Qantas flight at 9.45am Adelaide time took the majority of athletes and officials home from what team boss Kitty Chiller has described as the “toughest Games ever”.

Among the passengers were the nine athletes whose passports were returned on Sunday after a last-minute renegotiation regarding payment of fines for falsifying documents.

The athletes were detained by police overnight on Friday for close to 10 hours and charged with altering their Olympic accreditations – a practice Chiller said was widespread, and that she had failed to end.

She returns home with a question mark over her future, declining to answer when asked if she would stand down.

Australia’s eight gold medals, the same as London 2012 and the worst since Barcelona 1992, put them in 10th place on the medals table after aiming for 16 gold and a top five place.

Swimmer Josh Palmer was also on the passenger manifest, having been interviewed by Rio police for nearly six hours on Saturday over his claims he was robbed at gunpoint in Copacabana.

An Australian Olympic official said police accepted his version of events and no further action would be taken.

The Australian team spent their final night together in Rio at the athletes’ village, with Chiller lifting the alcohol ban.

“The team came back from the closing (ceremony) and had a really raucous night singing songs in the hub (at the village),” an AOC spokesman said.

“They absolutely raised the roof off building 23.”

-AAP