The Nigerian star had arrived Moscow from London.
Confirming the incident, Russian police said two loaders at Moscow’s Sheremetyevo Airport were the primary suspects.
Kanu reported the money missing when he reached Kaliningrad, where featured in a World Cup curtain raiser game organised by FIFA.
“The stolen cash was removed (from the loaders) and will soon be returned to the owner,” Irina Volk, spokeswoman for the Russian interior ministry, said.
The loaders, aged 30 and 36, face criminal investigation and could be sent to jail for up to six years.
Kanu played alongside ex-Manchester United and England star Wes Brown in a FIFA legends team against a Russian legends side.
The 41-year old did not mention the theft while speaking to the media in the Baltic city, where Nigeria will play their first game on June 16.
“The pitch is marvellous and, actually, that’s all you need as a player.
“The FIFA World Cup is the greatest football tournament on the planet – every team dreams of being part of it and I am sure it will be a very special event in Russia.
“Nigeria will be a big surprise, for sure. We have good young and talented players; they are hungry for victories and want to do well – for themselves and for the country.”