The 5,000 and 10,000 metres Olympic and world champion was recently laid low by illness and has decided to pull out of the Glasgow event in order to work on his fitness ahead of next month's European Championships in Zurich.
"I have taken the tough decision to withdraw from the Commonwealth Games," Farah, 31, said in a statement released by Team England.
"I really wanted to add the Commonwealth titles to my Olympic and World Championships, but the event is coming a few weeks too soon for me as my body is telling me it's not ready to race yet. Best wishes to my fellow athletes in Glasgow."
"The sickness I had two weeks ago was a big setback for me," he added.
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"Training is getting better here in Font Romeu but I need another few weeks to get back to the level I was at in 2012 and 2013."
Farah's withdrawal falls on the first day of competition in Glasgow and robs the event of a major draw.
The Somali-born runner became a household name in Great Britain when he took gold in the 5,000 and 10,000 metres at the 2012 Olympic Games in London.
"It is a real blow for any athlete to miss out on a major championships through injury, but to have fought so hard to regain full fitness and to have to take such a difficult decision at this stage is particularly hard," said Team England's chef de mission, Jan Paterson.
"We wish Mo all the very best and hope to see him back to his peak very soon.