Malaysian Ayuni, who won the gold medal with Nur Suryani Taibi in the 10 metre air rifle pairs in New Delhi four years ago, was due to compete in the 10 metre air rifle and 50m rifle prone events.
Team manager Musa Omar said he was left with no choice but to withdraw Ayuni from competition after the missing luggage, believed to be in London, failed to show in time for Monday's registration ahead of Thursday's start of competition.
"She was a gold medallist last time and now she won't even get a chance to compete. It is really painful for her. I just feel so sorry for her," Musa was quoted as saying by Malaysian media on Tuesday.
Commonwealth Games
Kerwood claims Glasgow gold - and now wants another
28/07/2014 AT 11:03
"We made a report when her bag did not arrive with the other luggage. We waited for three days... today is the last day for us to confirm the names.
"The rules clearly state that a rifle shooter must wear a jacket.
"We tried to borrow one but it did not fit her. We tried to make a new one but she said that she would need two months to get used to it."
Musa said Ayuni had been unable to stop crying and wanted to fly home immediately upon being told she would not be able to compete.
However, Musa said she would have to stay with the team in Scotland and watch Muslifah Zulkifli take her place in the 10m air rifle and Suryani, who competed in the 2012 London Olympics while 30 weeks pregnant, take over for the 50m prone.
"The licence for all her firearms is under her name. We cannot send her back immediately," Musa said.
"This is all so unfortunate. She's taking it badly. She is sad, we are all sad."
Tokyo 2020
The Top 10 Shooting Moments at the Olympic Games
27/04/2021 AT 11:14
Amber Hill not fearful of social media ahead of Tokyo 2020 Games
12/04/2021 AT 08:09