The Victor Harbor Goolwa Sea Rescue Squadron has apologised after concerns were raised after a training drill that entered the Encounter Bay whale nursery area on Sunday.
Five boats were involved in the training exercise which took place between about 10am and 12pm, launching from the Bluff Boat Ramp.
During the drill, the boats spent about 30 minutes within the whale nursery. No whales were spotted nearby at the time.
Squadron Leader Grant Williams said the exercise was used to familiarise squad members with rocks in the area in case of rescues and that most of the drill was carried out two to three nautical miles off shore.
"We did not mean to upset anyone because that's not what this was about," Mr Williams said.
"We are sorry if we upset anybody for entering the area at this time of the year. In hindsight we would definitely do it differently next time.
"We do not consider ourselves above regulations and we did not break any rules. Nothing we did was against any rules."
Mr Williams said the squadron were aware of the locations of two whale pairs when they entered the nursery area and that the closest any boats came to whales, was about 2.5 kilometres.
"We were not near any whales at the time and we all like whales," he said.
"The last thing we want to do is upset them. We are about saving lives and looking after boating people or anyone who happens to fall off rocks in the area while watching whales."
Mr Williams said the squad would continue training exercises but would avoid the whale nursery area.
In a separate incident earlier that morning, a recreational vessel was allegedly observed approaching a mother and calf whale pair off Middleton.
The boat has since been identified and the incident has been reported to the Department for Environment and Water (DEW).
A DEW spokesperson said that National Parks and Wildlife Service South Australia (NPWSSA) will investigate reports of breaches of legislation.
"At this point in time the NPWSSA has not received any footage of this incident," the spokesperson said.
The spokesperson added NSWSSA was aware of reports circulating on social media in relation to the Sea Rescue training event.
"A NPWSSA ranger had a positive and constructive conversation with Sea Rescue this morning [July 28] about the need to be mindful of whale presence at this time of year."
Spokesperson for Encounter Whales, Elizabeth Steele-Collins said it was unfortunate that two separate incidents had taken place on Sunday, the first day a new mother and calf were settling into the nursery area.
"It was also disappointing that the recreational fishing boat travelling at speed went towards the mother and calf and then followed them for a time," Ms Steele-Collins said.
"The nursery should be free from disturbances so a mother can be at ease to give birth and to feed and raise her young.
"The underwater noise generated by the motorised vessels travelling at speed in the whale's calving and nursery area would have been significant.
"These incidents seem to have been enough to unsettle the mother and cause her to move her calf to Petrel Cove where the pair were last seen on Monday at dusk.
"They appear to have now left the area , though we hope they will return."