Stocks in the National Bank of Greece fell almost 6%, while Piraeus and Alpha banks fell more than 5%.
IMF officials pulled out of talks with Greek politicians in Brussels on June 11, citing “major differences”.
Greece is seeking to avoid defaulting on a €1.5 billion debt repayment to the IMF.
The payment is due by the end of the month.
Shares on the Athens Stock Exchange had soared on June 11 amid renewed optimism about Greece’s talks with its creditors.
The index climbed more than 14% – the best performance in several weeks.
But the IMF’s withdrawal has dampened investors’ moods.
On June 12, Jeroen Dijsselbloem, president of the Eurogroup of finance ministers, said a deal without the IMF was “unimaginable”.
However, German Chancellor Angela Merkel urged all parties to continue negotiations.
Speaking at a business conference in Berlin, Angela Merkel said: “Where there’s a will there’s a way, but the will has to come from all sides so it’s important that we keep speaking with each other”.
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