The star, who currently plays for Belgian side Lokeren-Temse, was arrested on Monday morning as part of an investigation into the import of cocaine from South America to Europe, via the port of Antwerp.
As part of the investigation around 30 houses were searched in the province of Antwerp and in Belgian capital city, Brussels, according to Dutch paper De Telegraaf.
During the investigation Nainggolan's car was towed, among a number of other possessions.
"The investigation concerns suspected facts of importing cocaine from South America to Europe, via the port of Antwerp and its redistribution in Belgium," says the Brussels public prosecutor's office.
"We can confirm that the footballer Radja Nainggolan has been arrested.
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"As the interrogations are currently ongoing, no further comment will be made at this stage."
It's not the first time that Nainggolan has been linked with cocaine smuggling.
The report states that one of the midfielder's business partners in a private jet firm has been convicted of drug smuggling for terrorist organisation Hezbollah.
More recently, Nainggolan had been regularly spotted with people close to the drug world in Antwerp's nightlife.
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The 36-year-old has enjoyed a playing career at the highest level after leaving Belgium for life in Italy at the age of 17.
His big breakthrough came with Serie A side Cagliari before going on to join Roma in 2014.
It was in the Italian capital where Nainggolan would spend his best years, making over 200 appearances and scoring 33 goals.
He also played 24 times for Roma in the Champions League.
That earned him a big move to join Inter Milan for £32million in 2018, but despite scoring seven goals in 41 games, he left the club for two loan spells with former club Cagliari before returning to Belgium.
He did, however, win the Serie A title at the San Siro during the 2020/21 season.
Nainggolan was also a part of Belgium's golden generation, winning 30 caps in a side that featured Vincent Kompany, Eden Hazard and Kevin De Bruyne.
He now plays for Belgian second division side Lokeren-Temse, whom he joined last summer.