Mistura, who met the marines in prison yesterday, said that international law should have applied to the Italians and also expressed concern over the lengthy trial.
He said it should be borne in mind that the marines on the Italian commercial vessel were operating in a sensitive maritime region where six pirate attacks had been reported in the recent past.
"They had tried to send some signals. They shot in the water and fired warning shots, some of which went in the wrong direction," he told Karan Thapar at CNN IBN's programme 'The Last Word'.
He described it as an "accidental killing" and an "unfortunate incident which everyone regrets."
Mistura said he respected the Indian judiciary but believed international law should apply in the case.
Yesterday, the Italian minister met the marines, Latore Massimiliano and Salvatore Gir, in a Kerala prison and also called on Archbishop M Soosai Pacckyam in Thiruvananthapuram this morning.
He told reporters earlier that Italy also shared the safety concerns of Indian fishermen and would take steps to ensure that ships from his country would not stray into territorial waters, where traditional fishermen mostly engage themselves.