Inter's decision means that Nainggolan, who was also dropped by AS Roma at the start of this year, will miss Wednesday's match when third-placed Inter host second-placed Napoli in Serie A.
"FC Internazionale Milano can confirm that Radja Nainggolan has been temporarily suspended from football activity for disciplinary reasons," said the club in a statement, without giving further details.
Italian media said Nainggolan had arrived late for a training session.
The combative 30-year-old was signed from Roma in the summer for 38 million euros ($43.19 million) plus Nicolo Zaniolo but has not made the expected impact.
He missed Inter's first two league matches of the season through injury but scored on his debut in a 3-0 win over Bologna.
He suffered another injury in the 1-0 derby win over AC Milan and, although he quickly recovered, it flared up again during the Champions League defeat at Tottenham Hotspur when he was substituted before halftime.
Nainggolan was dropped and fined by Roma in January after posting an Instagram video of himself drinking and smoking at a New Year’s Party.
After returning to the side, he helped Roma to reach the Champions League semi-finals but there was more disappointment when he was left out of Belgium's World Cup squad by coach Roberto Martinez.
That prompted Nainggolan to end his international career and blame Martinez's decision on a personality clash.
Nainggolan was also upset at the way he was treated by Roma, saying in an interview this month that he was "bitter" that the club had wanted to sell him.
(Writing by Brian Homewood; editing by Clare Fallon)
