Many projects sell at over VND60 million ($2,367.80) per square meter, rising to even VND150 million in some places, it said in a recent report.
The smallest apartment (40 sq.m) at Heritage West Lake to the northwest of West Lake is priced at VND3.8 billion.
A 30-square-meter unit at Masterise West Height in the southwest of the city starts at VND1.8 billion.
"Apartments continue to attract interest from buyers with residential needs and medium- and long-term investors," the ministry said.
Prices have been rising rapidly since the end of last year due to a widening gap between supply and demand. Many projects have seen prices rise by 20-25% in the last six months.
Prices on the secondary market jumped by 17% year-on-year in the first quarter, the highest increase ever recorded, according to property consultancy CBRE.
The average price of old apartments is VND36 million per square meter. But no new apartment projects were launched during the first quarter.
The Ministry of Construction wants the city People’s Committee to identify and punish speculators who have been driving up property prices.
But analysts called it a futile quest and suggested it should be tackled with policies such as imposing taxes for ownership of multiple properties.