The alert warned of a "dangerous event of exceptional intensity," as the Category Four storm passed at a distance of around 100 kilometres.
The islands could expect winds that could reach 120 kilometres per hour, up to 100 millimetres of rain and waves of between six to eight metres, forecasters said.
St Barts is a French overseas territory, as is the French part of St Martin, which is divided between France and the Netherlands.
President Emmanuel Macron scheduled a top-level meeting in Paris late today to review the situation, especially regarding security, the president's office told AFP.
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Prime Minister Edouard Philippe, Defence Minister Florence Parly and Interior Minister Gerard Collomb were scheduled to take part.
The French interior ministry said 410 gendarmes and 80 police have been deployed, with 150 more gendarmes set to arrive after the hurricane leaves the area tomorrow.
Eleven people have been arrested for theft, it said.
All air and sea links with the two islands have been cut.
Irma is now heading for Florida, where a total of 6.3 million people have been ordered to evacuate, according to state authorities.
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