Al-Zawari, 49, was killed in a hail of bullets at the wheel of his car outside his house in the city of Sfax, 270km southeast of Tunis, in December 2016.
“The two people who carried out the assassination were identified – both were of Bosnian nationality,” Tunisian prosecution spokesman Sofiene Sliti said on Wednesday.
One of the suspects was arrested on March 13 in Croatia, he said, without giving details on the other.
Bosnia, which was consulted by Croatia, refused to allow its Balkan neighbour to hand over the suspect, said Sliti.
“We are in discussions with the Bosnian authorities [to convince them] to agree to deliver this individual, who is still in Croatia,” he said.
“We have been surprised to find, however, that the Bosnian authorities are refusing to hand over the arrested individual to Tunisia.”
Contacted by Al Jazeera, Bosnia’s ministry of internal affairs did not immediately respond.
Croatia’s ministry of internal affairs confirmed the arrest.
“Following his arrest, he was ordered to extradition custody, while the extradition procedure is under the jurisdiction of judicial bodies of the Republic of Croatia,” a spokesperson from Croatia’s interior ministry told local media.
Shortly after his death, Hamas said al-Zawari was a drone expert who had worked for the “resistance” for a decade.
The movement credited him with developing the Ababeel drones used against the last Israeli offensive on the Gaza Strip in the summer of 2014.
Leaders from both Hamas and the Lebanese Hezbollah group have accused the Israeli spy agency Mossad of assassinating al-Zawari.
Last November, during a press conference in Beirut, Hamas claimed Mossad agents carrying Bosnian passports were responsible for his murder.
According to their investigation, al-Zawari was under close surveillance by Mossad for four months before his assassination.
The full investigative report, which is published on Hamas’ website, includes details of how the killing was meticulously planned over three stages in 2015 and involved 12 individuals.
Israel has neither confirmed nor denied its activities abroad.
Israel has assassinated several of the Hamas movement’s members in the past.
In November 2017, al-Zawari‘s family denounced “silence” on the part of authorities and called on them to provide more details on the investigation into his killing.
Family and friends of Batsh accused Mossad of carrying out the killing in Kuala Lumpur on April 21.