Lumumba, the Central African country's first democratically elected prime minister after independence from Belgium in 1960, was assassinated by a firing squad in 1961 after his government - which lasted only three months -was overthrown.
The tooth was reportedly taken from Lumumba's body by a Belgian policeman, who claimed to have dissolved much of Lumumba's body in acid and burned the rest.
The tooth was handed over to his family in 2022.
A police officer present at the scene on Tuesday morning told Reuters that the coffin where the tooth had been was "open and empty" but could not confirm whether it had been stolen.
Lumumba is widely hailed as the nationalist activist who helped to end colonial rule.
For many in DR Congo, Lumumba is a symbol of the positive developments the country could have achieved after its independence.
Instead, it became mired in decades of dictatorship that drained its vast mineral riches.
Historians say Lumumba was a victim of the Cold War.
He promoted progressive policies and when he reached out to the Soviet Union for help in putting down a secessionist movement in the mineral-rich Katanga region, he fell out of favour with Belgium and the United States.
His assassination, blamed on separatists, cleared the way for the rise of Mobutu Sese Seko, who ruled the country he later renamed Zaire for decades until his death in 1997.
Even though Lumumba's killers were local, questions have persisted over the complicity of Belgium and the US because of his perceived Communist ties.
The culture ministry also did not specify on Tuesday whether the tooth had been stolen.
"The site has been secured, and an investigation is underway to determine the facts and identify those responsible," it said.
Lumumba's daughter Juliana Lumumba Amato described the vandalism as "a despicable and incomprehensible act" in a message to Reuters.
"Patrice Lumumba sacrificed his life for his country and the Congolese people", she said, adding that she was still waiting for information from the government
The DR Congo Minister of Communications did not respond to requests for comment.
with AP
