"I completely agree with the monks council about banning the insulting scenes," Hun Sen said in a speech at a Buddhist pagoda inauguration ceremony broadcast on the radio.
"(Broadcasters) should have let the Ministry of Cults and Religion check it first. We do not want such a story to happen again," he added.
Local human rights groups expressed concern that the cancelled television broadcast threatened freedom of expression, after rave reviews of the show that merges pop and rock music with more traditional and historical Cambodian tunes.
But Hun Sen applauded a compromise in which the rock opera's creators agreed to make three specific edits after meeting with clergy and government officials.
"It's good that they (the authors) found a solution by making an apology and a promise of change," Hun Sen said during his speech.
The show tells the story of a Cambodian-American man who returns after the demise of the 1970s Khmer Rouge regime to reconnect with his roots. While he is a monk, he falls into a doomed love affair with a pop singer.
After a successful run in the Cambodian capital Phnom Penh last November and December, organisers are in discussions to resume its broadcast and remount the production in tourist hub Siem Reap next year.
There are also plans for the opera to tour South Korea, Singapore, Hong Kong, Japan and the United States.