A deal was agreed with the 27-year-old but the Board of Control for Cricket in India (BCCI) have rescinded a decision to grant Pathan permission to play.
Chief executive David East told BBC Essex: "We're all a bit puzzled to be honest with you, but at the moment we're in limbo."
Northamptonshire have missed out on Virender Sehwag for the same reason.
Pathan needed a 'no-objection certificate' from the BCCI to play for Essex, which was initially granted only to be revoked shortly afterwards.
East added: "We'd thought long and hard about the player that we wanted, and you can see by the results that he's had in the IPL that he's a devastating cricketer.
"We're not just going to go out there and buy anyone, they've got to add some value to our team.
"If there isn't anyone available that will add value to our team then we won't do it."
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