He was accompanied by Italian Ambassador Giacomo Sanfelice, Consul General in Mumbai, Giampaolo Cuttillo and the ship's captain.
Mistura's meeting on Wednesday night with Chief Minister Oommen Chandy at Kottayam had failed to end the standoff over the issue, with both parties sticking to their stands.
Chandy told reporters after the meeting that the Italian minister maintained the incident took place in international waters and sought to raise the issue of compensation for the families of the victims.
He said the fishermen were killed in a "brutal manner" and that the compensation issue did not figure in the talks.
The Chief Minister also said there was no point in discussing the matter as "it is a murder case" and that the case would proceed by its legal process.
Chandy also said the Italian side wanted to meet the relatives of the fishermen, but were told that the situation is "not right" for it.
Meanwhile, the two naval guards are likely to be taken to Kollam on Thursday evening for being produced in court as the three day police custody ends on Thursday.