Japan's Foreign Ministry said the incident on Monday was serious and added that there had been a series of reports about North Korean boats engaging in "illegal fishing" inside the Japanese EEZ, Efe news reported.
The two countries don't maintain diplomatic relations.
The collision occurred about 350 km northwest of the Noto Peninsula in the Sea of Japan after the Agency's surveillance vessel alerted the North Koreans of having trespassed and ordering it to leave the area.
The patrol boat's crew members told state broadcaster NHK on Tuesday that the fishing boat approached suddenly and came into contact with their vessel.
The North Korean vessel sank upon collision, while its crew - initially thought to comprise 20 fishermen but later confirmed to include at least 60 - was rescued, the Japanese Coast Guard said.
The fishermen were subsequently transferred to another North Korean boat in the area. According to preliminary information, the government intended to take the North Korean sailors to Japan and interrogate them.
The Japanese surveillance boat - which escaped major damage and harm to its crew - had confronted the North Korean vessels while it was allegedly fishing for squid in the Japanese EEZ.
Hundreds of cases of North Korean vessels coming into Japanese waters have been reported in the last few years, with their fishermen often being rescued by the country's coast guards or found dead after having drowned.
North Korean fishermen are thought to venture away from their coast in search of bigger catch to make up for the lack of resources in their country or to meet state production quotas.
( With inputs from IANS )