The 19-year-old Gemili, one of the brightest prospects in British sprinting, said he had found out about Afilaka's situation on Friday in Barcelona, where he is attending the centenary celebrations of the International Association of Athletics Federations (IAAF).
A spokeswoman for UK Athletics said the organisation was undergoing a "performance restructuring" about which more information would be published early next week. She declined to give any further details.
"UK Athletics are making a couple of coaches redundant and I think my coach is subject to that but obviously as it just happened last night and I'm in Barcelona I don't know too many of the details," Gemili said at a news conference.
"I found out last night when I got a couple of Tweets on my phone and I haven't talked to (Afilaka) yet," he said, adding that he was not going to move to Loughborough where UK Athletics are looking to base their training operations.
"He has been one of the most important factors (in my development) and obviously it's a shame that he's lost his job.
"He's taken me to the next level and helped me a lot with my technique. Not just technical, lifestyle and nutrition and everything like that, just trying to be an elite athlete.
"But I'll still training with him; I can tell you that I won't be moving up to Loughborough.
"I'll still be based in London, keep doing what we're doing and try and run quick next year."
Gemili, a talented soccer player who spent time at Chelsea's academy as a defender, was the youngest member of Britain's Olympic team in London and narrowly missed out on a place in the 100 metres final.
"I'm training full time now, I'm also at university studying sports and exercise science and human biology," he said.
"It's quite challenging but I think it's going to help with my running, just knowing my body."
He ran 10.05 seconds to win the world junior title and is hoping to break the 10-second barrier in 2013.
"The main goal is outdoors, the European Under-23 championships (in Tampere, Finland in July), I hope to make the team and try and get a medal there," he said.
"And obviously if I'm lucky enough to get on the team for the world championships (in Moscow in August) I'd like to go there and do well as well and get myself in good shape to run hopefully quicker than I have this year.
"I'm not going to say a time but everyone always talks about sub 10, sub 10.
"I think sub 10 will happen when I understand my race a bit better. I think next year hopefully I should be in good shape to do it but I'm not going to say yes I'll do it or no I won't do it so who knows."
Making the switch from soccer to athletics was challenging and he had needed to do a lot of research into the 100 metres, including watching past races on You Tube, Gemili said.
"I learnt so much about sprinting and the history of it - just going and seeing what they did and what you're doing and trying to sort it out.
"The training is so much more intense. You're always tired and you get so much lactic acid and it's horrible but it is rewarding when you are able to go and compete and show everyone what work you've been doing."
Gemili said he had enjoyed being around past and present champions in Barcelona.
"I got to meet a lot of athletes and coaches," he said. "With so many legends in the room I wasn't going to miss an opportunity to introduce myself and get some photos."