Images of the police action, which saw officers smash through the gates of the compound with chainsaws, were broadcast live on the group`s television stations, Bugun and Kanalturk.
Brawls also broke out outside the compound, prompting police to use tear gas and batons against the demonstrators, including lawmakers from the main opposition Republican People`s Party (CHP).
Several arrests were made, the private NTV television channel reported.
CHP lawmaker Mahmut Tanal and Tarik Toros were seen negotiating with police chiefs who tried to cut the live broadcast.
"Dear viewers, do not be surprised if you see police in our studio in the next few minutes," Toros said.
An Ankara court on Monday appointed a board of trustees to manage the Koza-Ipek Group, seizing its 21 companies, including its media operations, as part of a crackdown on Gulen`s followers.
The move triggered demonstrations in both Ankara and Istanbul on Tuesday, with protesters chanting: "We will not be silenced."
The United States also weighed in to the controversy, voicing concern about media freedom in Turkey.
"When there is a reduction in the range of viewpoints available to citizens, especially before an election, it is a matter of concern," the US embassy in Ankara said in a tweet on Tuesday.
Ankara chief prosecutor`s office said in a statement the seizure was linked to an ongoing investigation into the conglomerate on suspicion of "terror financing", "terror propaganda" and other offences related to Koza-Ipek`s support for Gulen`s Hizmet (Service) movement.
Koza-Ipek CEO Akin Ipek denounced the move as "politically motivated", saying the government had failed to find any illegal activity during inspections of the company, whose businesses include media, energy, mining and construction.
Media rights groups have expressed concern over a further decline in press freedom since Erdogan became president in August last year after more than a decade as premier.
International journalists have been arrested and deported, while about 20 are currently detained on a variety of charges.
Turkish authorities have also ramped up their campaign against Pennsylvania-based Gulen in recent months.
Police in September raided Koza-Ipek`s media companies, briefly detaining six people including its CEO as part of a "terrorism probe" into the 74-year-old cleric.
Erdogan accuses Gulen of trying to topple him by persuading allies in Turkey`s police and judiciary to launch a vast probe into government corruption in December 2013, which led to the resignation of four ministers.
Turkey`s authorities responded by purging both the police force and judiciary of pro-Gulen elements and arresting news editors and businessmen.
The cleric, who left for the United States in 1999 to escape charges of anti-secular activities by the government of the day, denies the latest allegations.
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