The scheme is close to the islands of Lingay and Groay in the Sound of Harris.
Green MSP Robin Harper spoke against the proposal at the Scottish Parliament, as the scheme is in an area within a few hundred yards of a seal breeding site.
Mr Harper warned that approval would spark fresh requests to shoot seals locally. He also highlighted concerns about the effect on the local cormorant and otter populations.
The Green party lodged an amendment to the Marine Bill which would have prevented licences to shoot seals being granted to new fish farms where the developer chose to set them up within a certain distance of a known seal breeding site. The amendment was not backed by Parliament.
Mr Harper said:
I have no doubt if this is approved requests for a licence to shoot seals will swiftly follow.
David Bines who owns Lingay, said:
It’s absolutely ridiculous to site a fish farm next to high concentrations of predators and sensitive wildlife.
It goes against Scottish Government advice and the industry’s own code of practice.
The applicant, Andrew Rodger said:
We have, as all fish farmers do, the potential to manage seals by lethal method, but it’s not our chosen mode of operation. As a new business, we’re working towards standards which require us to follow guidelines for seal management.
On why it had to be located at his chosen site, he said:
The modelling we’ve done shows the site to be well positioned and the influx of water from Atlantic sources will help with the site’s fish disease management aspect. It’s also well located within the geography of the islands to be supported by a workforce.
Mr Rodger said the scheme would create seven full-time jobs.