FoE said that although the FSC set the "strongest available standard for new wood", it was not currently able to recommend the mark because "some FSC certificates are failing to guarantee rigorous environmental and social standards".
Head of climate at FoE UK, Ed Matthew, said: "We have been involved with FSC for years and are a big supporter of the scheme.
"However, six months ago we decided to stop recommending it. We have the highest standards for recommendations and recently we have had problems with some of the certifications."
He emphasised that FSC was "a very good standard" and said he hoped this was just a temporary blip.
A statement highlighting the issue was posted by FoE on its website in March this year. A recently updated version said: "Most FSC timber certifications are highly reliable – guaranteeing that wood has been sourced sustainably and improving forestry standards in many countries.
"However, we are concerned at reports that some FSC certificates are failing to guarantee rigorous environmental and social standards. As a result the mark's credibility is being undermined."
An FSC spokeswoman said that FoE UK had not officially withdrawn its membership from the scheme and maintained that, according to FoE's latest statement, the charity recognised that FSC certification is the strongest available standard for wood.
She said the FoE's statement "raises concern" about a number of certificates, but said it was taking particular care and working hard to reinforce the system in order to maintain and strengthen its credibility, minimising the possibility of flawed certification decisions.
"Feedback from stakeholder groups and the outcome of research into the causes for controversial certificates contributes to our efforts to strengthen and improve the system," she added, insisting that there was a complaints procedure in place to deal with stakeholders' concerns over certificates.
FoE said it is supporting a review of the FSC scheme to understand how it needs to be strengthened, in order to guarantee the highest environmental and social standards in all cases.
It said: "Until those changes have been identified and adopted we will not be able to recommend the FSC mark."
FSC credibility 'being undermined', charity claims
The credibility of the Forest Stewardship Council (FSC) standard has been "undermined", Friends of the Earth UK (FoE UK) has claimed.