The office of the president said in a statement Orlando Jorge Mera was gunned down by Miguel Cruz, who had been detained.
Officials gave no motive, and it was not immediately clear if Cruz had a lawyer.
"We express our deepest condolences," the office of President Luis Abinader said.
Following a call from a priest, heavily armed police officers took Cruz into custody at a church about 15-minutes' drive from the office where Jorge was shot.
When he was detained Cruz was wearing a helmet and bulletproof vest and kept his head mostly down. One bystander yelled: "You killed a good man. Murderer."
The victim came from a powerful political family.
Jorge was the son of the republic's former president Salvador Jorge Blanco, and his sister is a vice minister in Abinader's administration.
He was a founding member of the Modern Revolutionary Party, which his son also represents.
The family issued a statement saying Cruz had been Jorge's friend since childhood and that the minister had been shot multiple times.
"Our family forgives the person who did this. One of Orlando's greatest legacies was to not hold grudges," the statement said.
Police and emergency officials swarmed the office of the Environment and Natural Resources Ministry in the capital of Santo Domingo and barred entry as mourners gathered nearby.
"We are troubled by the situation," Jorge's ministry said in a brief statement.
Bartolome Pujals, executive director of the government's Cabinet of Innovation, wrote "His death is a tragedy".
"We Dominicans have to come together to achieve a pact for peace and peaceful coexistence. No more violence," he said.
Jorge, a lawyer, was appointed minister of the environment and natural resources in August 2020.
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