Waqa has represented Sri Lanka in the past at both fifteens and sevens level and he has subsequently been replaced by Alivereti Veitokani.
He will now miss the first two legs of the new World Series, in Dubai and Cape Town, with Fiji releasing a statement to explain the problem.
"It is with regret that we have removed Emori Waqavulagi from the squad to Dubai," read the statement ahead of the December 4-5 opener.
"It was brought to our attention that he has previously played for Sri Lanka at the 15s and 7s level and is therefore capped under World Rugby Regulations for Sri Lanka.
"We have subsequently sought an urgent ruling from the World Rugby Regulations Committee as to Emori's eligibility to play for Fiji and that process has commenced – however indications are that this will not be completed prior to the Dubai Sevens.
"Whilst World Rugby will launch a full investigation into his eligibility we have no other option than to exclude him."
(planetrugby.com)