Sunday markets and other second-hand markets will reopen in June 1, the Development and Investments Ministry said in a tweet on Thursday.
The ministry said the decision was approved by the scientific committee advising the government on the handling of the coronavirus pandemic.
Their operation will follow the same rule on hygiene that apply to farmers' markets, it added.
The central markets of Athens, Thessaloniki and Patras and the ten fishmarkets of the country that supply the majority of fresh produce in the wider market are continuing their operations as usual, their management said on Thursday.
The markets are however adherring to government directives for hygiene and the protection of the public, they added.