In an open letter to the International Olympic Committee (IOC) on Monday the NGOs, including Greenpeace, said there was mounting evidence the Tokyo Games were using timber through companies associated with illegal logging and human and labour rights violations.
They added that the organisers had not been transparent about the sourcing of the wood used in construction projects for the Games.
Tokyo organisers said the source rules developed had been the result of extensive consultations and were subject to constant regulation.
"Tokyo 2020 had extensive discussions with working groups comprising experts in environmental matters, human rights, labour laws, corporate social responsibility and other fields," a Tokyo Games spokesman said.
"In the series of discussions, we decided to have the meetings fully open to the media. We even took in feedback from the public in order to establish the sourcing codes."
The spokesman told Reuters previous allegations in April about the use of illegal timber had been taken back by some NGOs after a meeting with Tokyo Games officials.
SOURCING CODE
"Tokyo 2020 has published a general sustainable sourcing code and a sustainable sourcing code specifically governing timber.
"The Japan Sports Council and Tokyo 2020 sat together with the NGOs, who later withdrew the allegation after our thorough explanations," he said.
"Tokyo 2020 sourcing codes emphasise a compliance with laws and respect for human rights... We are preparing for a formal contact information service to address any further issues that may arise in the future."
This is not the first environmental hurdle for the Tokyo Games.
The relocation of the city's Tsukiji fish market, a popular tourist destination, to build an access road that will reduce the travel time for athletes has also experienced problems.
It has been delayed because of concerns about the clean-up of toxic pollution at its proposed new home, including unsafe levels of cancer-causing benzene.
(Reporting by Karolos Grohmann; Editing by Christian Radnedge)
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