Clips began to surface last week showing young children of Ctrip employees being roughly handled, and punished by being force-fed what parents claimed was spicy mustard at the company's Shanghai headquarters.
Shi Qi, a group vice president, and vice president Feng Weihua were suspended by Ctrip pending an internal investigation, according to a company letter circulated online.
A Ctrip spokeswoman told AFP on Wednesday that the letter was authentic.
Police last week said they had detained three daycare staff for suspected abuse.
The company said the daycare centre has since been shut.
Ctrip is China's biggest online booking site for air, rail and other travel. It bought British flight search app Skyscanner for $1.7 billion last year.
After the video of the abuse went viral, subsequent clips emerged showing irate parents trying to take revenge by forcing what appeared to be spicy mustard into the mouth of one of the accused female staff members, as police sought to hold them back.
Ctrip had outsourced daily operations of the daycare centre to Shanghai Women, part of a nationwide organisation that aims to protect women's rights in China.
"It is hard to imagine that we are coding upstairs and you are abusing our babies downstairs," wrote one man on Weibo, China's equivalent of Twitter, claiming to be the father of a child that attended the daycare.
He added that it had been very hard to get his child admitted to the daycare, which has a waiting list.
About 100 children, all aged below three, attended the daycare centre in the past three months, Ctrip said.
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