The costs stem from the July 7 tribute to the fallen pop icon at the Staples Center.
The mayor's office last week announced it was accepting donations to help offset the cost of the event to the city, while some Los Angeles officials said they thought Jackson's family or AEG, which owns the Staples Center, should help pay for the expenses.
"This is a world-class city, and we provide fire and police protection. Period. The idea that we would charge the family for a funeral is nonsensical," the Los Angeles Times quoted Villaraigosa as saying.
The mayor reportedly also dismissed the notion of having AEG pay the bill.
The Times said Villaraigosa criticized his office and the acting mayor for establishing a Web site asking for donations to help pay for the city's costs, while he was out of the country on vacation.
"I thought it was ridiculous, and that was the word I used when I called my staff from South Africa," the mayor said.
The Web site has since been removed, but the Times said it is unclear whether the $35,000 fans contributed to it would be returned.