The 36-year-old won the Rotterdam Open last week and became world No 1 for the first time since 2012.
But organisers in Dubai were hopeful Federer would play given he has a home in the city but tournament director Salah Tahlak has now confirmed the 20-time Grand Slam will miss the event to spend time with his wife Mirka and four children.
“I have been in touch with his agent and the last time we spoke he informed me that Federer would rather spend some quality time at home with his wife and kids than make the trip to Dubai,” Tahlak told Gulf News.
“He also said that this decision from the world No. 1 has nothing to do with Dubai, but it’s simply because he doesn’t want to take any chances during the build-up to his defence of the two titles in Indian Wells and Miami.
“In fact he has conveyed his willingness to come and play in Dubai next year.”
As alluded by Tahlak, Federer will return to tennis action in March to defend his titles in Indian Wells and Miami.
The field in Dubai will now be headed by world number 5 Grigor Dimitrov.
Lucas Pouille, Roberto Bautista Agut, Damir Dzumhur and Richard Gasquet are also set to feature at the ATP 500 event.