Wednesday's incident concerns a six-metre square area extending across the upper parts of a wall in an ancient house and a partition wall between two buildings, Pompeii's Archaeological Superintendency said.
Both walls were ancient but did not contain frescoes. The area was cordoned off and culture officials were carrying out technical checks to assess the damage, according to the superintendency..
Pompeii's archaeological superintendent Jeannette Papadopolous played down Wednesday's collapse.
"It's quite possible for these kind of events to occur in a vast archaeological site dating back two millennia, especially during such weather conditions.
"They should not generate excessive alarm or sensationalism," Papadopolous said.
Bondi was on Wednesday due to organise a meeting to create a Pompeii foundation to help with the sprawling site's upkeep.
Bondi faced calls for his resignation in November after the frescoed House of the Gladiators collapsed, sparking sharp debate over the future of the Italian cultural heritage.
Government officials denied the collapse was due to cuts in the culture budget and blamed local management problems at the site.
As recently as Tuesday, a 12-metre long portion of a garden wall surrounding the nearby House of the Moralist gave way.
Bondi warned against "useless alarmism" and said the situation in Pompeii was being "constantly monitored by experts."
"The collapse did not involve anything of artistic, archaeological or historical worth," he said in a statement, referring to the collapse at the House of the Moralist. The house derives its name from hectoring rules of etiquette inscribed on black panels in its dining-room, including: "Have respect for other men's wives."
The Italian government in 2008 declared a "state of emergency" at the fragile archaeological site of Pompeii - one of the best preserved in the world - saying it had fallen into disrepair.