The minister made the admission when journalists questioned him over the incident during the opening of a trading establishment in Kandy.
Rajapakshe said however, he saw nothing wrong in the journalist in question getting assaulted had he disrupted duties of the Navy.
He said a conclusion could be reached after receiving results of an ongoing investigation.
The minister said there was a serious issue as to why Rear Admiral Ravindra Wijegunaratne had gone to the port dressed as a civilian.
‘It was an act of piracy’
Wijegunaratne says the Navy had taken action to get two foreign ships detained by the protestors released.
The Navy has the responsibility of protecting ships and ports if they come under attack by pirates or terrorists, he said.
The Navy chief claimed it was an act of piracy that the two ships, one being the third largest vehicle carrier in the world, had been detained by the protestors for six days.
The vehicle importers will have to pay 400,000 dollars a day for the duration of their detention, he said.
When asked if he had attacked a journalist at the port, Wijegunaratne said that had he attacked a journalist, that person should have been in hospital by now.
He should have said which media institution he represented, the Navy commander said, adding that he has known for some time about the person in question and whom he has been representing.