Whistleblowers told BBC Scotland last week that surgical teams were prevented from seeing A&E patients to speed up times and hit targets.
Dr Catherine Calderwood was asked to visit the hospital by health secretary and city MSP Shona Robison.
She said the findings of her investigation would be made public.
Two Ninewells doctors told BBC Scotland that surgical teams were being bullied and prevented from seeing potentially seriously ill patients in the emergency department. They said hospital managers wanted these patients moved to the surgical department, so that a box could be ticket saying they had been discharged from A&E.
One doctor said they had "never experienced emergency care which is so aggressive in terms of getting patients out of the department", amid an "utter fixation to the four hour target".
During a Holyrood debate on the health service, Ms Robison said she had been given assurances by NHS Tayside about the situation at the hospital, but said she had asked Dr Calderwood to investigate "to restore confidence".
Dr Calderwood said: "While we have received reassurances from the board about the system here in Tayside, when serious allegations like these are made, it is absolutely right that they are fully looked into.
"I am here today with a completely open mind to listen to staff and look at the systems in A&E and the medical and surgical admissions units. I want to be completely satisfied that the reassurances provided by the board are correct and stand up to scrutiny.
"There will be an opportunity for staff, including trainees, to speak to me without management and on a confidential basis if necessary. I am equally happy to listen to views from any staff at NHS Tayside who wish to contact me outside of today's visit, to ensure that all views are listened to.
"This is an important issue, and I will consider the visit over the course of this week. As the Scottish government has confirmed, these findings will be made public."
Scotland's chief medical officer has visited Ninewells Hospital in Dundee to investigate claims about practices designed to manipulate waiting times.