"It was a very sad and unfortunate incident...We are sorry about it," Antony said, talking to reporters here.
Indian Coast Guard's patrol vessel ICGS Vaibhav had dashed against 'Sea Massiah', a trawler, 13 nautical miles from the Agonda coast of Canacona taluka in South Goa.
Six of the 23 crew of the trawler were killed in the mishap.
Defence Ministry will do everything to support the families of the dead fishermen and action would be taken against Coast Guard officials after enquiry is completed, Antony said.