Addressing a press conference for foreign journalists, Gotabaya said such ports are vital strategic centre and only Sri Lankan government should decide which military ships enter its territory.
He said even Chinese side have agreed that security operations should remain with Sri Lankan government and the issue was discussed with Chinese special envoy who visited him early this month.
The President said they are not worried about the commercial aspect but handing over security aspect can create issues with world powers.
Hambantota port was leased to a Chinese company for 99 years by previous government which India and western powers have been concerned about.
The Sri Lankan President reiterated his call for investment from countries including India and Japan.
He called for investment from Indian high tech companies in the IT sector and to use the potential within India.
Gotabaya added that their aviation department will discuss the Mattala airport as second international airport and currently there are no discussions of Indian involvement.
To a query on Sri Lankan Tamil refugees in India, he said that the government has been trying to bring them back and refused to comment on citizenship amendment bill saying it is internal matter of India.