Mr Li made his comments during his trip to Germany, where he and Chancellor Angela Merkel signed trade agreements.
Thousands of protesters, demanding fully democratic elections, have paralysed parts of Hong Kong.
The pro-democracy protests, which had tens of thousands of participants at their peak, had decreased in size over the past week, as the government and student leaders agreed to hold talks.
However, the government called off the talks on Thursday, saying the students’ refusal to end their protest had made “constructive dialogue” impossible.
Leaders of the student movement also called on supporters to return to the streets, saying they would escalate their campaign if the government did not agree to meet them.
China’s state media has strongly criticised the pro-democracy sit-in, describing it as an “illegal movement” driven by “evil forces”.
Speaking in a joint press conference with Mrs Merkel on Friday, Mr Li did not mention the protests directly.
However, he said: “Maintaining the long-term prosperity and stability of Hong Kong is not only in China’s interests but is mostly in the interests of the people of Hong Kong.”
“I am sure the people of Hong Kong and the government of Hong Kong have the competency to ensure the wealth and stability of society… [while] protecting residents from injury and property damage.”
He said there would be “no change” to the “high degree of autonomy” currently enjoyed by Hong Kong, adding that “Hong Kong’s affairs belong to the internal affairs of China”.
Mrs Merkel said: “The demonstrations have gone peacefully, and I hope it can remain that way.”
Mrs Merkel added that she hoped that “in a free exchange of opinions, solutions are found that satisfy the population in Hong Kong”.
The demonstrations are centred on how Hong Kong’s leader, known as the chief executive, should be elected.
The protesters want to be able to directly elect Hong Kong’s leader.
China has promised a public vote in the 2017 chief executive elections, but it says all candidates to be approved by a similar nominating committee – effectively giving Beijing the ability to screen out candidates.
A key organiser of the protest group Occupy Central, Benny Tai, told the BBC that the government should offer protests a “roadmap” towards fully democratic elections in Hong Kong.
“In our constitution, the Basic Law, we have been promised with universal suffrage… you do not have such things in other parts of China,” Dr Tai said.
Hong Kong’s mini-constitution came into effect after the former British colony was handed back to China in 1997.
It states that “the ultimate aim is the selection of the chief executive by universal suffrage upon nomination by a broadly representative nominating committee in accordance with democratic procedures”.