Seok Hae-Kyun, 58, the skipper of the Samho Jewelry, which had been captured by pirates in the Arabian Sea, was shot repeatedly as South Korean navy commandos stormed the vessel on 21January.
In the operation they freed 20 other crew members, shot dead eight pirates and captured five.
The five, including a man identified as Arai Mahomed, have been questioned in Busan in the presence of state-appointed lawyers.
"Because of conflicting testimony by the pirates, the investigation focused on who shot Captain Seok," a coastguard spokesman in Busan told news agency AFP.
He said Mahomed denied responsibility, although some of the crew pointed the finger at him.
"We have evidence supporting the fact that one of the five pirates shot Captain Seok," chief investigator Kim Chung-Gyu said, according to the South Korean Yonhap news agency.
Investigators are also looking into whether the pirates targeted the chemical carrier after learning that a South Korean supertanker owned by the same firm had been freed last year after a large ransom was paid.
The 300,000-tonne Samho Dream and its 24 crew were released after a reported 9 million dollar (6.6 million euro) payment.
The five pirates could face life in prison if convicted of shooting the Samho Jewelry's captain.
If he were to die, they could be sentenced to death, although South Korea has carried out no executions since 1997.
Captain Seok underwent two operations in an Oman hospital and was flown back to South Korea for another procedure.