Le Maire said on Thursday that he will ask the commission to reopen waters to French fishers from Saturday until they reach their quota.
The summer season opened on 1 June, but the commission announced that fishing the tuna with huge "purse seine" nets would end at midnight 9 June, rather than the scheduled date of 15 June.
"The commission has declared a zero tolerance approach towards overfishing and will take all necessary measures to ensure full compliance across the board," the EU body said.
"The closure of the purse seine fishery is necessary to protect the fragile stock of bluefin tuna and to ensure its recovery."
Following the decision, Le Maire said he was seeking an explanation from Brussels.
"The commission has to either provide formal proof that French trawlers have fulfilled their quotas... or allow them to reach their legally-authorised quotas."