"Amazing how a party that couldn't find a single Muslim worth fielding in Gujarat suddenly finds FDI in retail anti Muslim and cares about it," Omar wrote on micro-blogging site Twitter.
He said the party expresses sympathy with the Muslim community only when it "needs" their votes.
"They (BJP) find their sympathy for Muslims when they need votes in Parliament - nuclear deal and now FDI in retail," the Chief Minister said.
Omar had, earlier this year, said he wanted the states to decide whether they want to allow FDI in retail or not in their areas of jurisdiction.