China has sent fighter jets to patrol the border after the incident, in which a bomb hit a sugarcane field in Lincang in Yunnan province on March 13, killing five workers and injuring eight others.
It came days after Beijing warned of escalating violence near the border following a surge in ethnic conflict in the remote Kokang region in Myanmar's northeastern Shan state.
Beijing was a key backer of Myanmar's military junta while it was under Western sanctions, but President U Thein Sein has increased ties with other countries including the United States since launching political reforms in 2011.
Mr Li expressed "condolences and deep sympathies to the victims and their families" at his once-a-year meeting with journalists.
"At the same time, our government, the ministry of foreign affairs and the military have made solemn representations to the Myanmar side," he said.
"We have the responsibility and the ability to resolutely safeguard the security and stability of the China-Myanmar border, and we will resolutely protect the lives and property of our people," he said.
China's People's Liberation Army Air Force on Friday sent several fighter jets to "track, monitor, warn and chase away" Myanmar military planes flying close to the border, air force spokesman Shen Jinke was quoted by China's official news agency Xinhua as saying.
It cited Fan Changlong, vice chairman of the Central Military Commission, as telling the commander of Myanmar's military that Beijing will take "firm and decisive action" in the event of any repetition.
Chinese deputy foreign minister Liu Zhenmin summoned the Myanmar ambassador to Beijing, U Thit Linn Ohn, on March 13 night to protest against the deaths, the agency added.
Last month, Myanmar declared a state of emergency in Kokang in response to the conflict, which began on February 9.
The unrest has virtually emptied the main Kokang town of Laukkai, the epicentre of the fighting, with streets in the once-bustling frontier community transformed into a battleground.
More than 30,000 people have fled from Myanmar into Yunnan province, according to Xinhua.