A leading union had urged Nicola Sturgeon to order an inquiry into undercover policing in Scotland.
The current Pitchford inquiry will only probe allegations in England and Wales.
Experts have warned that information collected on hundreds of blacklisted Scottish workers could only have come from the police or security services.
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Gary Smith, from the GMB union, said: "Pitchford’s attempt to exclude us is a classic example of the UK not meeting its responsibilities to provide justice for Scottish workers who, when GMB last looked, are still part of the United Kingdom.
“The fact that the Pitchford Inquiry will not extend to Scotland is a kick in the teeth and an insult to the 582 blacklisted workers from Scotland, many of whom may have been spied on by the police.
“It is of the utmost importance that allegations of police involvement in the blacklisting of construction workers and environmental activists are thoroughly examined and this can only be done when looking at all part of the United Kingdom. The Scottish Government must launch its own inquiry to examine undercover policing in Scotland.”
The Metropolitan Police’s Special Branch included the Special Demonstration Squad (SDS), which has been linked to undercover spying on trade unions.
More than 30 workers from Scotland recently settled blacklisting claims against the companies involved for £1.6 million.
A Scottish Government spokesman said Scottish ministers were "extremely disappointed" that the inquiry would not look into Scotland.
"We continue to believe that a single inquiry across the UK is the most effective approach to provide a comprehensive and coherent investigation into these matters.
"We will now consider how best to take this matter forward.”