Former football federation head Sani Abdullahi and the three other officials are accused of mismanaging Nigeria's 900 million naira ($6 million) World Cup funds and spending $250,000 to charter a faulty aircraft to fly the national team from London to South Africa ahead of the finals in June.
The Economic and Financial Crimes Commission (EFCC) told the court the ex-officials also paid $800,000 in allowances to 220 delegates to the World Cup when only 49 were approved.
They also paid $400,000 to stage a friendly against Colombia in London shortly before the finals and incurred a $125,000 fine over a failed hotel deal in South Africa, the EFCC said.
All four pleaded not guilty to the 10-count charges preferred against them and asked the federal high court in the capital Abuja for bail.
Abdullahi, Amanze Uchegbulam, Bolaji Ojo-Oba and Taiwo Ogunjobi were rearrested on Monday, after they were first detained for questioning in July when their passports were seized following their sacking.
President Goodluck Jonathan initially banned the Super Eagles from international competition for two years after they failed to qualify from the group stages of the World Cup finals.
He later rescinded the decision, saying he had taken into consideration the views of ordinary Nigerians who appealed to him on his Facebook page, although there was also considerable pressure from football world governing body FIFA.
Thank you for reading 5 articles this month* Join now for unlimited access
Enjoy your first month for just £1 / $1 / €1
*Read 5 free articles per month without a subscription
Join now for unlimited access
Try first month for just £1 / $1 / €1