He said his office was informed of the problems only on Thursday last week, despite a series of weekly meetings between his staff and the organising committee.
Mr Paes's week got off to a rough start on Sunday when the Olympic village opened to a boycott from Australia, which refused to move in because of exposed wiring, leaking pipes, blocked toilets, unlighted stairwells and other problems.
The mayor's ensuing quip that he would have a kangaroo placed outside to make the Australians feel at home did not go down well, exploding into a controversy dubbed #kangaroogate on Twitter.
Mr Paes and the Australian delegation chief, Kitty Chiller, buried the hatchet on Wednesday, when he apologised for the construction hiccups and presented her a symbolic key to the city.
She gave him a stuffed kangaroo in return.
In similar tongue-in-cheek style, the Australians have also installed a kangaroo statue outside the village, alongside an ersatz emu.
But Mr Paes was clearly still smarting from Sunday's controversy. "It was an unacceptable mistake. Which is too bad, because that was the launch of the Olympics," he said.
"It wasn't a Brazilian in charge of the Olympic village. Only foreigners," he added.
"At least people can't say the Brazilians are disorganised. The boss was (Argentine national) Mario Cilenti."
Mr Cilenti, a sporting event manager serving as executive director of the athletes' village, has reportedly been sacked from the job, according to Brazilian media.
Rio2016 has not confirmed the reports.
The organising committee did not immediately reply to requests for comment on Mr Paes's interview.
Brazilian media reports have blamed disgruntled workers for the problems at the village, allegedly the result of sabotage aimed at exacting revenge for salary delays.
Fifteen of the 31 buildings had plumbing problems, ranging from leaks to toilets clogged by cement blocks.
More than 600 plumbers were dispatched to make emergency repairs.
Stoking further controversy, the Brazilian labour ministry said the emergency hires did not have proper working conditions and contracts.
Rio2016 said all problems with the village were fixed by Thursday evening.