"We have lodged a complaint with the European federation, with a copy sent to the global federation, for the refereeing commission to review the video of the match and judge whether the refereeing was deliberately in favour of Romania", said a statement from the Spanish body.
The two assistant referees were also Romanian.
Rugby Europe said in a statement on Monday (Tuesday NZT) that it is waiting for an assessment report by the supervisor of the match officials for the Belgium-Spain game, and will devote a "large portion" of a tournament committee meeting on Friday (Saturday NZT) to the "analysis of every stage of the Belgium v Spain game".
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"Rugby Europe has always operated the highest standards of match official selection whatever the competitions", said a statement on the organising body's official website.
Spain travelled to Belgium needing a victory - a fixture they won 30-0 last year - to finish above Romania and automatically qualify, joining Pool A at next year's tournament alongside Ireland, Scotland and hosts Japan.
There were ugly scenes after the game which you can see in the video above.
"It isn't just Spain who are the losers today", Spain coach Santiago Santos told LaLiga4Sports.
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Controversially, Vlad Iordachescu - from Romania, who qualified at Spain's expense - was in charge of the clash and appeared to make a series of contentious decisions in Belgium's favour.
He then offered his apologies to the ref for his side's actions, adding: "I am captain and I apologise for the persecution of the referee".
"The difference between penalties against us and for us was huge".
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Painter said Haarms brings a high level of energy as a shot-blocker on defense and can open up Purdue's offense with his mobility. The Bulldogs were down by three with a chance to tie after Purdue missed the front end of a one-and-one with 1.8 seconds to play.
Spanish back Brad Linklater pointed to the "Belgian aggression and irregular tackling that went unpunished" by the man in the middle who was appointed by Rugby Europe.