Deshmukh, a 40-year-old Indian national who had been in the country since January 2009, was stripped of his press card along with 10 other correspondents on February 15, a day after a major Tehran protest.
The demonstration was the most significant one in the Iranian capital in a year and was covered by AFP and most of the international media.
"Jay is a highly professional and experienced journalist.
His expulsion is incomprehensible and unacceptable," said AFP global news director Philippe Massonnet.