They said the state of the body found in the river was consistent with it being there since mid-February.
The manner of death has not been determined at this time, the medical examiner said.
Cunningham also called his mother at 9:12 a.m. that day, but she did not answer, Atlanta police have said.
The Fulton County Medical Examiner's Office has identified the body recovered in the Chattahoochee River in NW Atlanta late Tuesday to be missing CDC employee Timothy Cunningham.
Cunningham left work in the Atlanta office on February 12, saying that he was sick after learning he was passed over for promotion. The river had been searched previously, but people fishing spotted Cunningham's body and called 911 Tuesday.
Cunningham, a Harvard graduate, was wearing favorite jogging suit, officials said.
Police initially said that on the day Mr Cunningham was last seen alive, he had expressed disappointment to his supervisor about missing a promotion.
The case perplexed investigators because Cunningham's keys, cell phone, credit cards, debit cards, wallet and all forms of identification were found in his house, along with his beloved dog. Cunningham was known to collect these sort of items.
The local medical examiner has ruled the cause of Cunningham's death was drowning and there are now no signs of foul play, according to local police.
In announcing that his body had been found, authorities offered no hint about why he disappeared.
Cunningham's father told The New York Times in February that he'd been anxious about his son recently because he didn't seem like his usual self in conversation.
"We may never be able to tell you how he got into the river", Major Michael O'Connor of Atlanta Police told reporters.
"The most unusual factor in this case is that every single belonging that we are aware of was located in the residence", O'Connor said.
Cunningham had an impressive career in public health, and the Atlanta Business Chronicle named him one of 2017's "40 under 40".
The agency said he'd been deployed to work on numerous public-health emergencies, including Superstorm Sandy, the Ebola outbreak, and the Zika outbreak.