The Turkish men, who were working on a football stadium project, were seized in Baghdad's Sadr City area earlier this month, and militants presenting themselves as a Shiite group claimed the kidnappings in a video posted online.
"We demand the release of the kidnapped men and the end of such practices, which harm the image of Islam" in general and Shias specifically, Sistani's office said in a statement.
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Such actions also lead to "reducing the prestige of the state and weakening the elected government," the statement on Sistani's website said.
In the video, militants armed with submachine guns and wearing black uniforms, sunglasses and balaclavas stood behind men said to be the kidnapped Turks, identifying themselves as "Furaq al-Mawt," or "Death Squads."
And one of their demands was that Turkey order rebel forces to stop besieging four Shia villages in northern Syria.
This all indicates the militants are Shia, but could also potentially be an attempt to mislead, and the group's make-up and provenance were not immediately clear.
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The demands, addressed to Turkish President Recep Tayyip Erdogan, also included Ankara stopping "the flow of militants from Turkey to Iraq," and "the passage of stolen oil from Kurdistan through Turkish territory."
Iraq's autonomous Kurdish region is independently exporting oil via Turkey in a move the federal government considers illegal -- a point of contention between Baghdad and Ankara.
"If Erdogan and his party do not respond, we will crush Turkish interests and their agents in Iraq by the most violent means," the group said in the video, which lacked the polished production quality found in most militant propaganda in Iraq.
Dozens of Turks have been kidnapped and released in Iraq in the past 18 months by the Islamic State militant group, which overran large parts of the country last year.
But Sadr City is a stronghold of Shia paramilitary forces opposed to the militants.
Read: Militants claim kidnapping of 18 Turks in Baghdad: video
A soldier was killed last week when security forces clashed with the Shiite Ketaeb Hezbollah militia while searching for a person allegedly involved in the kidnappings.
The security command responsible for the capital said there had been intelligence that "one of the members of the gang that carried out the kidnapping" was on Baghdad's Palestine Street.
It did not identify the gunmen, but Al-Etejah television, which is affiliated with Ketaeb Hezbollah, said one of the group's facilities had been attacked by the Baghdad Operations Command on that street.
Baghdad turned to mostly Shia volunteer forces for support as IS advanced towards the capital in June 2014. Those groups have played a key role in halting and then reversing the militants' gains.
In doing so, the government empowered Shia militias, some with chequered human rights records, and spurred the creation of new ones, allowing them to act with near-impunity despite the fact they officially fall under government command.
Some people linked to the militias stand accused of criminal activities, including kidnapping, property seizures and murder.
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