Romanian referee Vlad Iordăchescu was confronted after Spain lost 18-10 to Belgium in Brussels, meaning Romania qualifies for the Cup in Japan next year.
"I don't want to think that rugby [has been fixed] to put us out. It must be understood that part of this dream has been taken away from us".
In a comment reported in the Daily Telegraph, Spain's coach Santiago Santos also questioned the referee's performance.
He said: "Everyone who has seen the game will judge the referee".
"The difference between penalties against us and for us was huge".
Not helped by a poor pitch worsened by snow in Brussels the night before, Santos's side struggled in the first half and went into their dressing room at halftime trailing 12-0. "I said to one of the players that Spain didn't lose today, rugby lost".
Spanish rugby federation president Alfonso Feijoo tweeted his disgust at the referee shortly after the contest. "He gave 10 penalties against us, the result comes from that", he posted on Twitter.
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It was known when they draw was made that they'd face both Japan and Scotland in a group that will no doubt be hard but one Ireland would expect to come out on top of.
Romania has played at every Rugby World Cup but never advanced beyond the pool stage.
Spain could still reach their second Rugby World Cup if they can advance through the play-off route.
Spain's loss saw Romania finish one point ahead of them in the Rugby Europe Championship, with Georgia lifting the trophy after winning all five of their matches.
Social media was quick to hint at dark conspiracy theories given the nationality of the man overseeing a qualifier involving a team in direct competition with his country's own World Cup bid.
The appointment of Iordachescu was made by Rugby Europe, rather than governing body World Rugby, with some reports suggesting that Spain had asked for the Romanian officials to be changed given the possible outcomes of the fixture in Brussels.