A foreign ministry official said on Monday the huge bill was "for air transportation and other costs".
The "other costs" relate to a medical check up in Dubai before flying to Japan with two relatives and a lawyer.
The three - an anti-war activist, an aid worker and a journalist - arrived home traumatised in a blaze of publicity on 18 April after a week-long ordeal at the hands of their Iraqi captors.
Amid an extraordinary backlash criticising them for being "reckless" and for costing the government time and money, they later released a statement apologising for causing trouble to the nation.
A lawyer for the group, Sayo Saruta, said they had already paid a total of $4000 in hotel and medical fees.
They will also pay a total of $18,200 for round trips between Tokyo and Dubai for the relatives and lawyer and one-way air fares for the three, he said.
Two other Japanese hostages - a journalist and peace activist - were also released unharmed in Iraq on 17 April.