"The fire started between the 22nd and 23rd floors of the 25-story building under construction," a source in the Emergencies Ministry told RIA Novosti.
More than 200 workers were evacuated from the site, ITAR-Tass reported.
RIA Novosti said one worker sought medical help after suffering smoke inhalation.
The fire, which engulfed less than 200 feet, was put out by midday, RIA Novosti said.
Officials said the fire could have been caused by a malfunction of a fan heater.
RIA Novosti said another skyscraper caught fire in Moscow in April.