The girl's coach said an official had called her over-the-knee dress "too seductive".
A Facebook post detailing the incident was shared widely, causing outrage.
The Malaysian Chess Federation told local media the accusation was under investigation.
The girl was participating in last month's National Scholastic Chess Championship in Putrajaya, just south of Kuala Lumpur.
Afterwards, her coach, Kaushal Khandhar, wrote a long public Facebook post saying an arbiter interrupted her game to tell her she was violating the competition's dress code.
"The tournament director deemed my student's dress to be 'seductive' and a 'temptation from a certain angle far, far away'," he said.
Mr Khandhar addressed his angry open letter to the Malaysian chess community, but it soon spread across the country and worldwide.
Zuraida Kamaruddin, an MP for the National Justice Party, criticised the organisers for not making a proper statement in response, according to Malaysia's the Star newspaper.
"I am very agitated about the issue. I feel for the young girl as if she were my own daughter," she said on Monday.
Mr Khandhar also posted a picture of the outfit, without showing the face of the girl, who he said was "extremely disturbed, and embarrassed".
He said she was given the opportunity to buy some trousers to continue competing the next day, but as the shops were closed, she was forced to withdraw from the event.
Datuk Heng Seai Kie, an adviser for the government's Department of National Unity and National Integration, told the Star that the organisers should not act as "moral police" by telling girls what to wear.
"Playing chess has nothing to do with dressing, as it is a healthy activity, and from the photo, she was decently dressed," she said.
The World Chess Federation's guidelines says competitors must comply with a "high-standard dress code", but it does not specify what this means.
Mr Khandhar has given the tournament director until Tuesday to publically apologise, or, he said, legal action would be launched.