Dr Catherine Calderwood was sent to investigate at the Dundee hospital after a whistleblower claimed surgical staff were prevented from seeing A&E patients to keep waiting times down.
She said she was satisfied that care at the hospital was not target-driven.
However, she criticised communication between A&E staff and other teams.
Whistleblowers told BBC Scotland last week that surgical staff had been bullied and "physically prevented" from seeing patients in the emergency department.
The matter was discussed in Holyrood after staff claimed surgeons were not allowed to assess patients until they had been moved to the surgical department, so hospital managers could "tick a box" saying the patient 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".
Dr Calderwood said she would be making a number of recommendations to prevent "misunderstandings", which she said had been caused by communication between emergency staff and specialty teams not always being "as good as it could be".
However, her report said she was "satisfied that the principles that underpin NHS Tayside's emergency department model are patient safety and outcome-focused, not target-driven".
She said: "There is no evidence to support the allegation that patients are admitted to speciality wards, or speciality doctors are unable to see patients within the emergency department, purely to achieve targets.
"NHS Tayside has also confirmed that surgeons and physicians regularly attend the A&E department to assess patients.
"The hospital has made significant improvements in patient safety, including a reduction above the national average in hospital deaths.
"The emergency department team assured me that improved patient waiting times and consistent attainment of the 98% target is a by-product of early senior review, decision-making and focused investigations."
Dr Calderwood said she would return to the hospital in six months to ensure her recommendations are acted on.
Scotland's chief medical officer says she found "no evidence" of waiting times manipulation during a visit to Ninewells Hospital.