The move comes with Ospreys and Scarlets at loggerheads with the WRU after the two professional sides did not sign the new Professional Rugby Agreement (PRA) by the imposed deadline of 8 May.
The WRU has since announced it will move away from a model of four evenly funded professional sides and implement a new two-tier funding system.
It is a move Ospreys and Scarlets have described as a U-turn that has "created more destabilising and debilitating uncertainty in our game".
The agreement has been signed by Dragons and also by Cardiff, who were last month taken over by the WRU after they temporarily went into administration.
The WRU insisted the new PRA offered a better deal for the regions but Ospreys and Scarlets said they had asked the governing body for assurances the takeover "will not disproportionally benefit Cardiff and disadvantage the independent clubs".
After Ospreys and Scarlets did not sign in May, the WRU says it has taken "the difficult but necessary decision" to issue the formal two-year notice to terminate the current PRA agreement, in particular, to proceed with its debt refinancing with its bank.
Reports have suggested the WRU intends to cut a team from its professional tier.
Welsh rugby's governing body has not confirmed or denied whether this is part of its plans, stating it hopes a long-term resolution will be decided by September.
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