Clubs are required to provide accurate details of training sessions and player whereabouts so that they are available for testing at all times.
City have allegedly failed to ensure its information was accurate on three occasions.
The FA has a 'three strikes' policy and the most likely punishment is a fine.
It is understood the information was not updated following a change to training routines.
BBC Sport's Simon Stone
The fact City have accepted the charge is not a surprise.
Doping is a word that attracts big headlines and they are even greater when it is attached to one of the world's leading football clubs.
However, as I understand it, the three breaches of the whereabouts rule were relatively low level.
Clubs are responsible for a number of teams - senior, women, under-23 - and one infringement by each would be enough to trigger a charge.
Still, it is slightly embarrassing for the Blues, who are likely to receive some sort of fine.

We are aware that this interactive video may not work on some older browsers. You can find a non-interactive version of the content below.
In this interactive video, Robert Opie - the founder of the Museum of Brands, Packaging and Advertising in London - outlines some of the main reasons why we change what we buy.
The arrival of the domestic freezer, of washing powder, and of cheaper imports all affected the sort of items on sale and popular among UK consumers.
The interactive elements to this video also explore how ownership and ranking of some of the biggest brands in the UK is changing.
The video works best in full screen
Click on the links below to read the extra information used in this video in a non-interactive format:
What in the world does China own?
Top tips on freezing food, BBC Good Food
Annual survey ranking the top 20 consumer brands in the UK
Museum of Brands, Packaging and Advertising

Speaking to BBC Radio 4's Today programme, he said: "The only response can be: 'yes, Mr President'."
Gen Petraeus resigned as CIA director in 2012 following an extramarital affair with his biographer.
It later emerged he had shared classified material with her.
He served as a senior officer under Presidents Bush and Obama. He was the commander of US and Nato forces in Afghanistan, before retiring from the military to take the top position in the Central Intelligence Agency.
Asked if he thought Mr Trump had the correct temperament to be the US President, he said: "It's up to Americans at this point in time not only to hope that that is the case, but if they can, endeavour to help him."
He then indicated he would personally serve under Mr Trump if asked.
"If you're asked, you've got to serve - put aside any reservations based on campaign rhetoric... and figure out what's best for the country," he said.
"I've been in a position before where a president has turned to me in the Oval Office in a difficult moment, without any pleasantries, and said 'I'm asking you as your president and Commander in Chief to take command of the international security force in Afghanistan.'
"The only response can be: 'yes, Mr President,'" he continued.
A number of media outlets have linked the retired general with positions in the new administration.
A report in The Guardian last week linked Gen Petraeus to the race for secretary of state, citing diplomatic sources.
Mr Trump has been putting together his administration made up of friends, family, and former rivals - but several key positions, including secretary of state, remain open.
General Petraeus was indirectly critical of some of Donald Trump's rhetoric during the presidential election campaign, describing the president elect's anti-Muslim comments as toxic.
However, he said he had heard good things from those who have been speaking with Mr Trump since the election result.
"It's interesting that those who have been talking to him have said, you know, he's very personable, very hospitable, very gracious guy, full of questions and dialogue," he said.
He also suggested that Mr Trump could forge closer ties with Russia, comparing his political position to that of President Nixon's overtures to China in the 1970s.
"Only Nixon could have gone to China. Anyone else would have been criticised from the right," he said.
"I think that the current president would have been criticised from the right had he tried some of the kinds of outreach that, in fact, President-elect Trump may pursue."
But he warned that any such outreach should be attempted "with your eyes wide open".
Manchester City have accepted a Football Association anti-doping charge after failing to notify officials of player whereabouts for drugs testing.
[NEXT_CONCEPT]
Advancing technology and manufacturing techniques are among the ingredients of our changing consumer tastes.
[NEXT_CONCEPT]
General David Petraeus, one of the United States' most prominent military officers, has indicated he would be willing to serve in President-elect Donald Trump's administration if asked.