Access to the Unesco-listed archaeological site will be suspended between midday and 5pm before reopening "to protect workers and visitors", she said.
"It's highly likely that we will take the same measure tomorrow [Saturday]," the minister said.
Temperatures are expected to reach 40ºC in Athens on Friday and Saturday, but at the summit of the Acropolis human bodies feel much more heat, she added.
Other popular tourist sites surrounding the Sacred Rock on which the Acropolis stands, such as the Ancient Agora, will remain open.
The Acropolis, which has seen a major rise in visitor numbers in recent months, is normally open from 8am until 8pm every day.
A summer heatwave is hitting several Mediterranean countries, with forecasters predicting the mercury to soar past 40ºC in northern and western Greece.
Authorities have in recent days taken measures to cope. Red Cross volunteers were deployed at the Acropolis on Thursday to hand out water bottles and help visitors suffering from the heat.
Shelters were set up near the entrance at the start of the week to protect the thousands of sightseers who come to admire the Parthenon from the Acropolis.
Authorities have warned about a greater risk of fires, particularly in regions where strong winds are expected.
Greece suffered major wildfires in 2021 as an exceptionally intense heatwave gripped the country.