Iskandarov was sentenced to 23 years in jail in October 2005, and had his appeal denied in January this year.
Iskandarov was first arrested in Moscow in December 2004.
The statement says the EU is "particularly concerned" about the circumstances of Iskandarov's transfer and arrest in Tajikistan in April 2005, which it says "remain unclear."
The EU also asked for further information from the Tajik authorities about some aspects of the court proceedings and the fact that the appeal procedure was not open to the media.
The EU Iskandarov's case sends "a mixed message" about democratic reforms and respect for human rights in Tajikistan.