The shipment was heading for Diyala province in eastern Iraq, Police Chief Lieutenant General Hadi Rzeich Kassar said in a televised statement.
From there, the pills were intended to be distributed to other provinces, including the northern Kurdish region, Mr Kassar said.
Police forces affiliated to the Anti-Drug Department acted on tips from informants once the shipment left Syrian territories, he added, saying investigations were under way.
“This quantity of pills would have impacted health and youth and contributed to crime if it entered any province,” he said, while standing next to a handcuffed man in yellow prison jumpsuit who turned his back to the camera as the pills were spread on a big wooden table.
The seizure is one of the largest to have been made in Iraq amid continuing efforts to combat smuggling. Early this week, authorities seized 30 kilograms of the synthetic drug crystal meth in the southern province of Najaf.
Drug trafficking and abuse have been growing rapidly in Iraq since the 2003 US-led invasion that toppled Saddam Hussein, posing a challenge to the country's security forces.
Security and health officials blame what they describe as successive weak governments, as well as widespread corruption among security forces, porous borders and a lack of co-operation between government agencies as the main reasons for the rise.
Since 2003, Iraq has been transformed from being a corridor for smuggling drugs to neighbouring countries to a place where consumption is hitting unprecedented levels.
According to Iraq officials, Captagon has become the second most widely used drug in the country, having overtaken tramadol, heroin and hashish. Crystal meth is also widely used in Iraq, accounting for 60 per cent of the country’s drug trade.