Spain's loss means that Romania qualifies for the 2019 World Cup as they finished second on 14 points at the expense of Spain who finished third with 13 points in the Rugby Europe Championship standings.
Spain must now beat Portugal in a playoff to maintain any hopes of reaching the 2019 tournament in Japan, with the victor facing Samoa in a two-legged tie.
But FER also said it will file a complaint to tournament organiser Rugby Europe about the refereeing, and request video of the match be analysed to check if decisions were "deliberately partial to favour the interests of Romania".
"Our game was stopped continuously, the Belgians benefited from many more decisions", he said after struggling to calm down his incensed players at the final whistle with even the Belgian players coming to Iordachescu's rescue.
Another penalty further bolstered the home side's lead in the 50th minute and Spain only came alive with 10 minutes remaining, forcing the only try of the game through Gautier Gibouin.
Spain's coach Santiago Santos was equally furious.
Del Potro to take on Federer at Indian Wells
Although he went down a break twice in the third set he stuck around and began to prey on Coric's inexperience. Yet the same can not be said for a Del Potro who looked so formidable at Indian Wells this evening.
At full-time, Spain players confronted referee Vlad Iordaschescu along with his two fellow Romanian assistant referees.
Irate Spanish players confronted Romanian referee Vlad Iordăchescu at the end of the match with a photograph revealing one Spaniard pushing the match official.
Rugby Europe released a statement on Sunday confirming the appointments were made before the Rugby Europe Championship, and confirmed during the tournament based on refs' performances. Instead, Romania remained one point ahead of Spain despite a 25-16 loss to Georgia on Sunday.
"I'm the captain and I would like to apologise for what happened with the referee", Nava said.
World Rugby told BBC Sport it would not comment on the match until it had received a full review, however vice-chairman Agustin Pichot posted on Twitter saying: "I'm going to watch the game and of course there will be an explanation". Japan is 5-1 in their tests against Romania. Georgia already automatically qualified.