The charges relate to the discovery by the Economic and Financial Crimes Commission of USD 9.8 million (9.2 million euros) and 74,000 pounds (USD 91,000, 85,000 euros) in cash at a property in the northern city of Kaduna.
He was also charged with failing to make a "full disclosure" of his assets and for unlawfully transporting the cash to the city. He pleaded not guilty.
Judge Ahmed Mohammed, sitting at the federal high court, remanded Yakubu in custody until next Tuesday when he will hear a bail application.
The charges against Yakubu, who ran the NNPC from 2012 to 2014 when Goodluck Jonathan was president, are the latest strike against senior figures in the oil sector.
Former oil minister Diezani Alison-Madueke was recently accused in a separate case of diverting more than USD 150 million from the NNPC, whose operations have long been considered opaque and corrupt.
President Muhammadu Buhari was elected two years ago vowing to stop the plunder of state funds by corrupt politicians and public officials in the country of 180 million people.
The main opposition party, however, has accused him of conducting a political witch-hunt because many of those arrested and charged are opposition party members or served in the previous administration.