The drugs were blown up together with the ship on Friday in an operation witnessed by President Uhuru Kenyatta from a helicopter overflying the Indian Ocean.
Experts involved told Capital FM News that the vessel was mounted with explosives which were detonated some 16 nautical miles south of the coastal town of Mombasa.
The Head of State on Thursday warned that “the Port of Mombasa will no longer be a passage for the importation of illicit drugs.”
“Tomorrow, I will lead security agencies in destroying a ship seized with heroin valued at Sh1 billion last month.”
He said the incident will serve as a lesson to those who bent, “on ruining our children. We do not care who owns the ship or the drugs.”
“We will not allow drug barons to destroy the future of our young people. We will track and deal with them decisively.”
The drugs were extracted from the 1,800 litres of the ship’s diesel reservoir on July 15 where they were concealed when it was intercepted off the Kenya Coast in Lamu by Kenya navy officers.
On April 25, Australian Navy sailors patrolling the coast of Africa seized another haul weighing more than one tonne on a suspicious sailing boat.
The estimated the street value of that heroin haul was put at $290 million (over Sh20bn).
Crew from HMAS Darwin boarded the wooden boat east of Kenya and discovered 46 sacks of heroin hidden among bags of cement.
The Navy said the drugs from the dhow were taken aboard HMAS Darwin.
President Kenyatta has vowed to enhance the war against drug trafficking where Mombasa is worst hit among other major towns in the country.