Construction at a tennis arena was stopped while work was partially suspended at the velodrome, the ministry said in a note, citing a "grave and imminent danger to the physical safety of workers."
The move comes as Rio races to complete projects with less than 500 days to go before the games.
The velodrome has been previously singled out as amongst the most delayed Olympic projects, although officials have recently stressed work was back on track.
The safety issue at the velodrome involved an access ramp being too steep, while at the tennis arena work was stopped due to missing guard rails, the ministry said.
RioUrbe, the body responsible for procuring and tendering the venues, said in a statement that the issues would be resolved by the end of the week and that the final delivery time of the projects would not be affected.
(Reporting by Rodrigo Viga Gaier, reporting by Stephen Eisenhammer; Editing by Bernard Orr)
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