Colonel Gulmurod Khalimov commanded the Central Asian nation's special-purpose police known as OMON, used against criminals and militants. He disappeared in late April, prompting a search by Tajik police.
He reappeared Wednesday, vowing to bring jihad to Russia and the Unites States as he brandished a cartridge belt and sniper rifle, in a professionally made, 10-minute video clip posted in social networks.
"Listen, you dogs, the president and ministers, if only you knew how many boys, our brothers are here, waiting and yearning to return to Tajikistan to re-establish sharia law there," he said, addressing Tajik President Imomali Rakhmon.
Rakhmon has run Tajikistan, the poorest post-Soviet nation that neighbours Afghanistan, since 1992. He used Russian support to crush Islamist guerrillas in a 1992-1997 civil war and tolerates little dissent in his country of 8 million.
"We are coming to you, God willing, we are coming to you with slaughter," said Khalimov, a 40-year-old native of the Tajik capital Dushanbe. He spoke in Russian, sitting in front of a palm tree, and sported a new beard. It was not clear which country he was in.
Tajik police could not be reached for comment. OMON police plan to issue a statement condemning Khalimov, several officers who had served with him told the Tajik service of US-funded Radio Liberty.
Khalimov said he had been trained by elite Russian "spetsnaz" forces in Moscow and US special forces in America.
"Listen, you American pigs, I've been three times to America, and I saw how you train fighters to kill Muslims," he said, patting his rifle. "God willing, I will come with this weapon to your cities, your homes, and we will kill you."
He lambasted Tajiks working in Russia. "You have become the slaves of infidels," he said.
Both Russia and NATO, alarmed by the threat of radical Islam to predominantly Muslim Central Asia, have stepped up military drills with the region's post-Soviet nations.
The International Crisis Group think-tank estimates around 4,000 Central Asians fight for Islamic State.
But Khalimov's defection shows that some local security units cannot be trusted if threats can come from insiders, not just insurgents, said Kazakhstan-based Central Asia analyst Alexander Knyazev."I think Islamist propaganda will now exploit Khalimov's example in full," he said, warning that volatile neighbouring Kyrgyzstan faced similar problems.