Ten timber firms have said they have "no confidence" in the ability of Natural Resources Wales (NRW) to manage forestry.
In a joint letter of complaint to the Welsh Government they called for an immediate review.
They said they relied on NRW for more than half their supply of wood and ministers should consider removing forestry from its responsibilities.
NRW said it accepts it had "significant issues" and will be meeting firms.
Confor, which promotes forestry and wood, said in the letter to Environment Minister Lesley Griffiths that the biggest timber processing companies in Wales had recently discussed their concerns.
It described the move as a "hitherto unprecedented occurrence".
The leaked letter from Confor's national manger for Wales, Anthony Geddes, has been signed by companies including Kronospan and Euroforest Ltd.
They said they had "no confidence in the ability of NRW to deliver a commercially viable, sustainable and commercially-driven service".
The letter claimed 12,000 jobs in the rural economy and £100m new investment over the next five years were at risk.
It urges an immediate review of NRW's management of forestry and to consider the case of removing forestry from the organisation's structure.
NRW was created in 2013 out of a merger of environmental bodies, including the Forestry Commission in Wales.
But it has been embroiled in a scandal over sales of timber to three firms in recent years without going to the open market. Two of these firms have signed this letter.
Its new chief executive admitted "serious failings" had occurred after criticism from auditors and AMs.
It led to the NRW chairwoman resigning and it is understood NRW's board will this week discuss the findings of a report commissioned from independent auditors Grant Thornton to find out what happened.
Plaid Cymru's environment spokesman Llyr Gruffydd said the letter was a "significant development" and called for an independent review to decide whether it is still appropriate for NRW to continue to manage the commercial forest estate in Wales
"If the inquiry finds that a change is needed then it should offer alternative models for the government to consider," he said.
"If it concludes NRW is the appropriate body then it must make clear recommendations as to how to improve relations with the sector."
Conservative environment spokesman Andrew RT Davies AM, said the letter came as no surprise and that NRW was "no longer fit for purpose".
A Welsh Government spokesman said: "We do not comment on leaked correspondence."
Clare Pillman, chief executive of Natural Resources Wales, said: "We fully accept that we have had some significant issues in our commercial forestry operations.
"We are taking these very seriously and have left no stone unturned in getting to the bottom of these issues, which is why we commissioned independent experts to carry out a thorough review, which will conclude very soon.
"Our relationship with our forestry partners is very important to us and we will be meeting with them in the near future to discuss our plans for improvements."