The raids on Koza-Ipek Media sparked fresh concern about press freedom in Turkey, which is gearing for snap legislative elections in November, its second in five months.
Six people have been arrested and a warrant has been issued for the conglomerate's chief executive, Akin Ipek, who is thought to be in Britain, the state-run Anatolia news agency said.
The swoop came a day after a court in Turkey's Kurdish-dominated southeast ordered two British journalists working for US-based Vice News to be remanded in custody on terror charges.
Ipek Media Group owns the Turkish dailies Bugun and Millet, the television channels stations Bugun TV and Kanalturk and the website BGNNews.com and is close to Erdogan's political rival, the US-based Muslim cleric Fethullah Gulen.
Masked police entered 23 offices as well as Ipek University in Ankara belonging to its parent company Koza Ipek Holding "as part of a terrorist investigation into Fethullah Gulen", Anatolia said.
They were accused of "providing financial support to and disseminating propaganda for a terrorist organisation," Anatolia added.
Speaking on Kanalturk on Tuesday, Ipek denounced the operation as "baseless" and "funny", adding: "If they (police) are able to find even a cent of illicit money, I am ready to hand my company over to them."
- 'Concern over Turkish democracy' -
The move was the latest targeting supporters of the powerful "Hizmet" (Service) movement headed by Gulen, a former ally-turned-foe whom Erdogan accuses of trying to create a "parallel state" with the aim of overthrowing his government.
"I'm worried that operations targeting the media will create great concern across the world about the state of democracy in Turkey," he added.
For several years Gulen, whose movement brings together a wide range of interests, from schools and media to finance, was seen as a close ally of Ergodan and his Islamic-rooted AKP.
But in 2013 the authorities blamed Gulen for corruption allegations that rocked Erdogan and the ruling elite, and the government launched an all-out war against him and his supporters.
In December, police arrested dozens of people in raids on other media outlets with ties to Gulen. The pro-Gulen Samanyolu TV (STV) chief Hidayet Karaca has also been remanded in custody on charges of leading a terrorist group.
- 'Alarmingly false' -
As Erdogan and his ruling Justice and Development Party (AKP) prepare for elections on November 1 under the shadow of a major offensive against Kurdish militants, opposition journalists have complained of a squeeze on all critical media.
The two Vice News British reporters and their translator, an Iraqi national, have been charged by a court in the southeastern city of Diyarbakir with "engaging in terror activity" on behalf of the Islamic State extremist group.
Vice News condemned the charges as "baseless" and "alarmingly false", while leading rights groups have called for the immediate release of the reporters.
A senior Turkish official said the Turkish government played no role in the arrests and is "not pleased" the three are being held, a senior official said Tuesday.
In Washington, US State Department spokesman Mark Toner urged Turkey in general to "uphold universal democratic values."
"That includes freedom of the press, due process and access to media information," he said.
"We've made our views often and clearly to the Turkish government," said Toner. "I'm not going to get into any specific diplomatic exchanges about this case we may have had. But they're aware of our feelings about this."
The EU's foreign service expressed concern over the arrests, calling for an "independent and transparent" investigation.
Erdogan caused outrage in the run-up to June 7 elections by saying Cumhuriyet newspaper editor-in-chief Can Dundar would "pay a heavy price" over a front-page story which it said proved Turkey had sent arms to Islamist rebels in Syria.
"You can't hide the truth even if you silence all the newspapers," Dundar wrote on Twitter Tuesday.
The front page of the anti-government Sozcu daily carried blank columns signed by its columnists in protest at the "unprecedented pressure on the media, the likes of which was not seen even during Turkey's coup era."
Meanwhile, Deniz Ulke Aribogan, an academic who hosted a TV show on state-run broadcaster TRT, said she had been fired over a tweet criticising the latest raids.
Milliyet daily has recently dismissed two high-profile columnists -- Kadri Gursel and Mehves Evin -- after they wrote pieces critical of the government.