"Both India and China are helping us at this very crucial time when we are facing an unprecedented economic crisis," Gunawardena said.
"The president (Ranil Wickremesinghe) informed the cabinet that this matter will be diplomatically resolved by talking to all sides. Both are important friends."
The vessel is to spend about a week at Hambantota taking in fuel and other supplies and will not undertake any work while in Sri Lankan waters, Gunawardena said.
Another minister, Manusha Nanayakkara, told the same press conference that 18 previous such port visits to Sri Lanka had been made by Chinese research vessels and that the Yuan Wang 5 was stopping "only for bunkering".
There was no immediate comment from the Indian High Commission in Colombo.
However, New Delhi last week made it clear that it will closely monitor "any bearing on India's security and economic interests and takes all necessary measures to safeguard them".
India remains suspicious of China's growing influence in its southern neighbour Sri Lanka, which owes large amounts of money to Beijing for infrastructure projects, including the $1.4-billion Hambantota Port.
Two Chinese submarines berthed in Sri Lanka in 2014 despite Indian objections. Since then, there have been no such Chinese submarine visits to Sri Lankan ports.
Sri Lanka gave a Chinese company a 99-year lease on the port, located along the main East-West international shipping lanes, in 2017 after being unable to keep up with debt repayments on the facility.
Sri Lanka defaulted on its $51 billion in foreign debts in April and has since opened bailout talks with the International Monetary Fund.
The country's 22 million people have been enduring severe shortages of food, fuel and medicines since late last year when the government ran out of foreign exchange to finance most imports.
President Gotabaya Rajapaksa, whose brother Mahinda Rajapaksa borrowed heavily from China while president from 2005-15, was forced to flee and step down last month when protesters overran his palace.