Under a previous verdict, Martinovic killed Djukic to get her flat.
Zekan said the Croatian services had beat him, threatened to tear off his arms and legs and "throw me to the fishes", adding that they had threatened his family as well.
He said the Croatian services had forced other members of Martinovic's unit to falsely accuse him as well, even though as commander he had not allowed attacks on civilians or setting houses on fire.
Martinovic is on retrial because the Supreme Court, only five days before his extradition to the Hague tribunal in August 1999, quashed a conviction handed down by the Zagreb County Court.
Dragan Raspudic was also convicted for the Djukic murder, serving a 10-year sentence.
The trial will resume with his testimony in October.