Two of the company's choppers piloted by Ashley Jenkinson and Michael James collided about 40m off the ground and crashed on January 2.
Mr James had been coming in to land with six passengers and Mr Jenkinson was taking off with seven people on board.
Mr Jenkinson, 40, died in the crash along with his passengers - British couple Ron and Diane Hughes, 65 and 57, and Sydney mother Vanessa Tadros.
The occupants of Mr James' helicopter were injured by flying glass after the windscreen shattered.
Operating for the first time since the tragedy, Sea World said their fleet's safety systems have been fully assessed and approved by the Civil Aviation Safety Authority and were cleared to begin operating some weeks ago.
"In many ways today is a difficult day for all of us as we pay our deepest respect to Vanessa Tadros, Diane and Ron Hughes, our friend and late chief Sea World Helicopters pilot Ash Jenkinson, their families and those who suffered physically and mentally in the accident," director John Orr-Campbell said in a statement.
"I know Ash would have wanted to be flying with us today.
"Helicopter flying is what we do and our staff wanted to get back to work and continue to provide the service to those who want to fly with us."
Initial investigations into January's incident found 23 seconds of radio silence may have contributed to the collision.
The Australian Transport Safety Bureau found no recordings of radio calls between the pilots moments before the incident.
A final report into the crash is not expected before September 2024.
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