The group – which included women from Australia, the UK and New Zealand – was checked for evidence they had recently given birth after a baby was found in a bin at Doha airport on 2 October.
Qatar’s government said on Friday that “standard procedures were violated”.
It also offered its “sincerest apology” for what the women went through.
Australian Foreign Minister Marise Payne called the referrals for prosecution an “important step”.
“The statement of the government of Qatar is consistent with our expectations for contrition, accountability and determination to avoid any repeat of this disturbing episode,” she said.
The incident came to light earlier this week after some of the Australian passengers spoke out and foreign governments said they were appalled.
The women said they were ordered to disembark the Sydney-bound Qatar Airways flight at Hamad International Airport.
They were then taken to ambulances on the tarmac and told to remove their underwear before being examined.
The women said they were given no information by officials and that they did not have an opportunity to provide informed consent.
Female passengers on nine other flights were also reportedly examined.