The Whitman campaign says such disputes are not uncommon in high-stress workplaces.
"Meg's record of accomplishment in business, including her success at leading eBay from a 30-employee startup to a Fortune 500 company, speaks for itself," said campaign spokeswoman Sarah Pompei in a statement issued to the Associated Press.
The two women reportedly overcame their differences and the employee continues to work at eBay.
The story, posted on the Times website, said Whitman became angry and pushed Young Mi Kim as she was helping Whitman prepare for a media interview for which Whitman felt unprepared.
Kim reportedly threatened to sue after the incident three years ago and later agreed to a mediated settlement that is not disclosed.
Kim left the company for about four months and returned to eBay. She is now a senior manager for corporate and executive communications.
In an e-mailed statement to the Times, Kim said she and Whitman had overcome their differences.
"Yes, we had an unfortunate incident, but we resolved it in a way that speaks well for her and for eBay," Kim told the newspaper. "And ultimately, I came back to the company, which is not something I had to do."