A statement issued by a Qatari diplomat singled out Belgian authorities for criticism and insisted that "inaccurate" information had been used.
Eva Kaili, a Greek MEP, is one of six people arrested after raids that uncovered at least 1.5 million euros ($1.6 million) in cash, Barrons reported.
The money was allegedly linked to a Persian Gulf state, and the EU parliament last week suspended Qatar's access to the institution.
"The decision to impose such a discriminatory restriction that limits dialogue and cooperation on Qatar before the legal process has ended, will negatively affect regional and global security cooperation, as well as ongoing discussions around global energy poverty and security," said the diplomat.
"We firmly reject the allegations associating our government with misconduct," the statement added.
"Qatar was not the only party named in the investigation, yet our country has been exclusively criticized and attacked."
"We have observed this week's selective condemnation of our country with great alarm," the statement said.
Belgian prosecutors said they had been investigating EU parliament corruption for more than a year before the raids and arrests of the past 10 days.
"It is deeply disappointing that the Belgian government made no effort to engage with our government to establish the facts once they became aware of the allegations," said the diplomat.
The statement highlighted the "close" relationship with Belgium.
"Our nations cooperated during the Covid-19 pandemic and Qatar is an important supplier of LNG to Belgium," it emphasized.
MNA/PR