The developments come as Iranian President Hassan Rouhani arrived in Switzerland as part of a visit to Europe in which Iran is seeking greater cooperation with the continent after the US withdrawal from the Iranian nuclear agreement.
Iran's foreign minister dismissed the attack plot as a "false flag ploy" created to overshadow Rouhani's tour.
The 38-year-old man and a 33-year-old woman, identified only as Amir S. and Nasimeh N., were charged with attempted terrorist murder and preparation of a terrorist act, it said.
Three people also were detained for questioning in France, but two of them were released Monday with no "incriminating elements" uncovered, a French judicial official source said.
Rouhani is also due to visit Austria, which now holds the six-month presidency of the European Union, and hosts the detained Iranian diplomat.
"Iran unequivocally condemns all violence and terror anywhere, and is ready to work with all concerned to uncover what is a sinister false flag ploy", he said.
The couple, described by prosecutors as being "of Iranian origin", were carrying 500 grams (about a pound) of the volatile explosive TATP along with a detonation device when an elite police squad stopped them in a residential district of Brussels.
"The terrorist diplomat, who is the station chief of the Ministry of Intelligence and Security (MOIS) in Vienna, has been stationed in Austria since August 2014", a source from the Committee of Security and Counter-terrorism of the National Council of Resistance of Iran (NCRI) said in a statement sent to Al Arabiya English.
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NCRI is an umbrella bloc of opposition groups in exile that seek an end to Shi'ite Muslim clerical rule in Iran.
Yet the administration has downplayed whether its recent words of encouragement equate to an unequivocal call for regime change like the MEK desires.
TATP, the explosive that Belgian authorities said was found in the suspects' vehicle, has been used in several terror attacks in Europe in recent years, including the 2016 bombings in Brussels that killed 32 people.
Trump's recent appointment of John Bolton, who spoke at a MEK rally before he became national security adviser, and Giuliani, a regular MEK headliner, are seen as moves that could strengthen the group's bid for USA backing.
Former House Speaker Newt Gingrich and former Democratic New Mexico Bill Richardson headlined Saturday's event in Paris alongside Giuliani.
The People's Mujahedin, formed in the 1960s to overthrow the shah of Iran, fought the rise of the mullahs in Tehran following the 1979 Islamic revolution.
A report by The New Yorker in 2012 revealed that the United States had covertly trained MEK members in Nevada during the Bush administration, an operation that required the utmost secrecy due to the organization's official classification as terrorist.
Belgium has been on high alert since the smashing of a terror cell in the town of Verviers in January 2015 that was planning an attack on police.